Phosphorus Stereochemistry Research Articles

Discovery and characterization of stereodefined PMO-gapmers targeting tau

Antisense oligonucleotides (ASOs) are an important class of therapeutics to treat genetic diseases, and expansion of this modality to neurodegenerative disorders has been an active area of research. To realize chronic administration of ASO therapeutics to treat neurodegenerative diseases, new chemical modifications that improve activity and safety profiles are still needed. Furthermore, it is highly desirable to develop a single stereopure ASO with a defined activity and safety profile to avoid any efficacy and safety concerns due to the batch-to-batch variation in the composition of diastereomers. Herein, a stereopure PMO-gapmer was developed as a new construct to improve safety and stability by installing charge-neutral PMOs at the wing region and by fully controlling phosphorus stereochemistries. The developed stereopure PMO-gapmer construct was applied to the discovery of ASO candidates for the reduction of microtubule-associated protein tau (MAPT, tau). Sequence screening targeting MAPT followed by screening of optimal phosphorus stereochemistry identified stereopure development candidates. While evaluating the stereopure PMO-gapmers, we observed a significant difference in safety profile among stereoisomers in which only one phosphorus stereochemistry differs. These results further highlight the benefits of developing stereopure ASOs as safe and well-characterized candidates for clinical studies.

Modeling of a near-attack conformation of oxime in phosphorylated acetylcholinesterase via a reactivation product, a phosphorylated oxime

At the present, only four antidotes are in use in therapy for poisoning by organophosphorus compounds: 2-PAM, HI-6, obidoxime and trimedoxime. Numerous compounds have been designed and synthetized to be more effective reactivators than those currently in use. Many of those new compounds fail at the enzyme level because interactions formed within the AChE active site are not favourable ones that lead to a successful reactivation. The approach in which the modeling of a phosphorylated oxime (POX), a product of successful reactivation in the AChE active site, may be a way to better understand the role of active site residues during the process of formation of the Michaelis type of complex between an enzyme and oxime. After reactivation, a change in phosphorus stereochemistry occurs leading to a different spatial arrangement of attached substituents, now including an oxime. To study interactions between the AChE oxyanion hole and a phosphorylated oxime, an S203G mutant was used to avoid the steric hindrance caused by the catalytic serine. In this way, the POX could be positioned close to the oxyanion hole. In the final step, the oxime without a phosphoester moiety was transferred into the phosphorylated AChE and molecular dynamics was used to test the stability of the near-attack conformation of the oxime near the phosphorylated serine.

Efficiency of bis-amidate phosphonate prodrugs

Bis-amidate derivatives have been viewed as attractive phosphonate prodrug forms because of their straightforward synthesis, lack of phosphorus stereochemistry, plasma stability and nontoxic amino acid metabolites. However, the efficiency of bis-amidate prodrug forms is unclear, as prior studies on this class of prodrugs have not evaluated their activation kinetics. Here, we synthetized a small panel of bis-amidate prodrugs of butyrophilin ligands as potential immunotherapy agents. These compounds were examined relative to other prodrug forms delivering the same payload for their stability in plasma and cell lysate, their ability to stimulate T cell proliferation in human PBMCs, and their activation kinetics in a leukemia co-culture model of T cell cytokine production. The bis-amidate prodrugs demonstrate high plasma stability and improved cellular phosphoantigen activity relative to the free phosphonic acid. However, the efficiency of bis-amidate activation is low relative to other prodrugs that contain at least one ester such as aryl-amidate, aryl-acyloxyalkyl ester, and bis-acyloxyalkyl ester forms. Therefore, bis-amidate prodrugs do not drive rapid cellular payload accumulation and they would be more useful for payloads in which slower, sustained-release kinetics are preferred.

Catalytic Asymmetric Synthesis of P-Stereogenic Phosphines: Beyond Precious Metals

AbstractMetal-catalyzed asymmetric synthesis of P-stereogenic phosphines is a potentially useful approach to a class of chiral ligands with valuable applications in asymmetric catalysis. We introduced this idea with chiral platinum and palladium catalysts, exploiting rapid pyramidal inversion in diastereomeric metal–phosphido complexes (ML*(PRR′)) to control phosphorus stereochemistry. This Account summarizes our attempts to develop related synthetic methods using earth-abundant metals, especially copper, in which weaker metal–ligand bonds and faster substitution processes were expected to result in more active catalysts. Indeed, precious metals were not required. Without any transition metals at all, we exploited related P-epimerization processes to prepare enantiomerically pure phosphiranes and secondary phosphine oxides (SPOs) from commercially available chiral epoxides.1 Introduction2 Copper-Catalyzed Phosphine Alkylation3 Copper-Catalyzed Tandem Phosphine Alkylation/Arylation4 Nickel-Catalyzed Phosphine Alkylation5 Proton-Mediated P-Epimerization in Synthesis of Chiral Phosphiranes6 Diastereoselective Synthesis of P-Stereogenic Secondary Phosphine Oxides (SPOs) from (+)-Limonene Oxide7 Conclusions

The role of P 3s2 lone pair (E) in structure, properties and phase transitions of black phosphorus. Stereochemistry and ab initio topology analyses

An approach merging crystal chemistry and density functional theory (DFT) electron localization function (ELF) taking P 3s2 lone pair (E) into account induces a full renewal of stereochemistry of black phosphorus, its crystal network evolutions and phase transitions under increasing pressures from atmospheric up to 32 GPa. Orthorhombic (Cmce) black P at ambient pressure, shows a packing of puckered [P]n layers - orthogonal to [010] - separated by a large free interspace (3.071 Å), which actually is partially filled by lone pairs (E) (P-E ~ 0.8 Å). Each P exhibits its lone pair pointing outside the [P]n layer, sandwiching it between two [E]n layers into a new stacking sequence … [EP2E]n … denoted O-[PE]n. The free interspace between [EP2E]n layers is much smaller 1.858 Å but allows sliding along [001]. The pressure evolving up to 2.66 GPa, all structural details have been followed and reported, including the layer thickness reduction along [010] and the sliding along [001] of consecutive layers.A mechanism for the phase transition occurring around 5.5 GPa is proposed. Depicted in the trigonal system the new layered phase R-[PE]n involves a bond rearrangement through E-E layer in zigzag phosphorus layers and P-E rotation and alignment with the A3¯ axis. Now, the phosphorene layers have P-E patterns oriented towards each other in their interspace.A very particular phenomenon occurs around ~11 GPa the lone pair centroid Ec (P-Ec = 0.73 Å) splits into three partially occupied sites Ed around the A3¯ axis which explains observed variations in properties at this critical pressure. So, we claim that there are two trigonal phases, R1-[PE] up to 11 GPa followed by a second form R2-[PE] directly caused by lone pair displacement from Ec to Ed and its influence on layer stacking.A further layer sliding brings the phosphorus atomic layers close enough to each other to establish new P-P bonds and then to cause an ultimate transition to cubic system, with a new structure, isostructural to Po. The mechanisms of the transitions are detailed.

Synthesis and Bioactivity of the Alanyl Phosphonamidate Stereoisomers Derived from a Butyrophilin Ligand.

Aryloxy phosphonamidate derivatives of a butyrophilin 3A1 ligand are stimulants of Vγ9 Vδ2 T cells. However, when bonded to an aryl ester and an amine, the phosphorus is stereogenic, and past compounds were studied as racemates. To determine the impact of stereochemistry on the activity, we now have prepared phosphonate derivatives of l- and d-alanine ethyl ester, separated the diastereomers, and evaluated their biological activity as single stereoisomers. The results demonstrate that phosphonamidates substituted with l-alanine stimulate Vγ9 Vδ2 T cells at lower concentrations than the racemic glycine counterpart, while those derived from d-alanine require higher concentrations. All four diastereomers are more active than charged phosphoantigens such as HMBPP. Surprisingly, only a 2-fold difference was observed between the l-alanine phosphorus isomers, with the R P isomer more potent. This suggests that the small phosphoantigen scaffold reduces but does not eliminate dependence upon phosphorus stereochemistry for cellular activity.

ChemInform Abstract: Applications and Stereoselective Syntheses of P‐Chirogenic Phosphorus Compounds

AbstractReview: [183 refs.

Glutathione-analogous peptidyl phosphorus esters as mechanism-based inhibitors of γ-glutamyl transpeptidase for probing cysteinyl-glycine binding site

γ-Glutamyl transpeptidase (GGT) catalyzing the cleavage of γ-glutamyl bond of glutathione and its S-conjugates is involved in a number of physiological and pathological processes through glutathione homeostasis. Defining its Cys-Gly binding site is extremely important not only in defining the physiological function of GGT, but also in designing specific and effective inhibitors for pharmaceutical purposes. Here we report the synthesis and evaluation of a series of glutathione-analogous peptidyl phosphorus esters as mechanism-based inhibitors of human and Escherichia coli GGTs to probe the structural and stereochemical preferences in the Cys-Gly binding site. Both enzymes were inhibited strongly and irreversibly by the peptidyl phosphorus esters with a good leaving group (phenoxide). Human GGT was highly selective for l-aliphatic amino acid such as l-2-aminobutyrate (l-Cys mimic) at the Cys binding site, whereas E. coli GGT significantly preferred l-Phe mimic at this site. The C-terminal Gly and a l-amino acid analogue at the Cys binding site were necessary for inhibition, suggesting that human GGT was highly selective for glutathione (γ-Glu-l-Cys-Gly), whereas E. coli GGT are not selective for glutathione, but still retained the dipeptide (l-AA-Gly) binding site. The diastereoisomers with respect to the chiral phosphorus were separated. Both GGTs were inactivated by only one of the stereoisomers with the same stereochemistry at phosphorus. The strict recognition of phosphorus stereochemistry gave insights into the stereochemical course of the catalyzed reaction. Ion-spray mass analysis of the inhibited E. coli GGT confirmed the formation of a 1:1 covalent adduct with the catalytic subunit (small subunit) with concomitant loss of phenoxide, leaving the peptidyl moiety that presumably occupies the Cys-Gly binding site. The peptidyl phosphonate inhibitors are highly useful as a ligand for X-ray structural analysis of GGT for defining hitherto unidentified Cys-Gly binding site to design specific inhibitors.

Thiophostone‐Derived Brønsted Acids in the Organocatalyzed Transfer Hydrogenation of Quinolines: Influence of the P‐Stereogenicity

AbstractA new approach to Brønsted acid organocatalysis is described and is based on the use of thiophosphonic acids possessing both a chiral backbone and a chiral phosphorus function. The influence of the phosphorus stereochemistry on the enantioselectivity proved to be crucial in the hydrogen transfer hydrogenation of 2‐phenylquinoline with Hantzsch esters.

Phosphorothioate oligodeoxynucleotides: large-scale synthesis and analysis, impurity characterization, and the effects of phosphorus stereochemistry.

Large-scale synthesis of phosphorothioate oligodeoxynucleotides on Tentagel using a 'batch mode' synthesizer and beta-cyanoethyl phosphoramidite coupling followed by sulfurization with bis(O,O-diisopropoxy phosphinothioyl) disulfide (S-tetra) provides stepwise yields of 98-99% and results in phosphorothioate oligodeoxynucleotides that are 93-97% pure, as determined by PAGE, after reverse-phase high performance liquid chromatography (RP-HPLC) and 'downstream' processing. The purity of phosphorothioate oligodeoxynucleotides synthesized on Tentagel is significantly higher than those synthesized on controlled pore glass. Electrospray ionization mass spectrometry of the n-1 impurity isolated by preparative PAGE was used to establish that the n-1 impurity is a heterogeneous mixture of all possible single-deletion sequences, relative to the parent phosphorothioate oligodeoxynucleotide, and results from minor, though repetitive, imperfections in the synthesis cycle. Acid-catalysed depurination was found to occur both during the synthesis and during the post-synthesis detritylation, following RP-HPLC. Studies of hybridization affinity and biological mechanism of action using independently synthesized n-1 phosphorothioate oligodeoxynucleotides relative to the 15 mer LR-3280 showed that, in this case, the majority of the n-1 sequences had more than a 10 degrees C decrease in melting temperature with sense RNA compared to the n-mer, and they did not cause detectable cleavage of RNA by RNase H in HL-60 human promyelocytic leukaemia cells. P stereoregular phosphorothioate oligodeoxynucleotides are not significantly more active than their stereorandom counterparts and thus their use in clinical studies seems unwarranted.

Nucleic Acid Containing 3′-C-P-N-5′ Ethyl Phosphonamidate Ester and 2′-Methoxy Modifications in Combination; Synthesis and Hybridisation Properties

Novartis Pharmaceuticals, Central Research Laboratories, Hulley Road, Macclesfield, Cheshire, SK10 2NX, UKFax +44(1403)323307; E-mail: robin.fairhurst@pharma.novartis.comReceived 29 January 2002Synlett 2002, No. 5, 03 05 2002. Article Identifier: 1437-2096,E;2002,0,05,0763,0766,ftx,en;D01702ST.pdf. © Georg Thieme Verlag Stuttgart · New YorkISSN 0936-5214Abstract: The preparation of thymidine-thymidine and thymidine-5-methylcytidine dinucleosides containing a 3 -C-P-N-5 ethylphosphonamidate ester linkage, with defined phosphorus stere-ochemistry, in combination with a 2 -methoxy substituent in thelower sugar residue, is described. Incorporation of these dinucleo-sides into DNA oligonucleotides and the effect upon duplex stabil-ity with complimentary RNA is reported.Key words: antisense, modified oligonucleotides, nucleosides,phosphorus, stereoselective

Synthesis of individual glutamate-containing phosphonamidothionate stereoisomers

The acquisition of the individual stereoisomers of chiral phosphonothioic acids is anticipated to reveal the significance of phosphorus stereochemistry upon the inhibition of metallocarboxypeptidases as well as their utility as chiral and stereoselective inhibitory probes. Two methods for preparing individual glutamate-containing phosphonamidothioic acid diastereomers have been identified. One method achieves the resolution through fractional crystallization of the intermediate 9-fluorenemethoxy phosphonamidates while the second does so through chromatographic resolution of intermediate β-(acylmercapto)ethyl phosphonamidothiolates.

Mechanism of adenylate kinase. What can be learned from a mutant enzyme with minor perturbation in kinetic parameters?

The structural and functional roles of threonine-23 in the chicken muscle adenylate kinase (AK) were investigated by site-directed mutagenesis coupled with proton nuclear magnetic resonance (NMR) and phosphorus stereochemistry. The residue is potentially important because it is conserved among all types of AK and is part of the consensus P-loop sequence, 15GXPGXGKGT23. A mutant enzyme T23A (replacing threonine-23 with alanine) was constructed. Analyses of conformational stability and proton NMR indicate that the side chain of this residue contributes little to the structure of AK, which suggests that the side chain of Thr-23 does not play a structural role. The steady-state kinetic data of the mutant enzyme T23A showed no change in kcat and only 5-7-fold increases in Km and dissociation constants. Such minor changes in kinetic data are insufficient to suggest a functional role of Thr-23. However, two-dimensional NMR analyses of WT.MgAP5A and T23A.MgAP5A complexes indicated that the side chain of Thr-23 is in proximity to the adenine ring of the ATP moiety in the WT.MgAP5A complex in solution. In addition, T23A showed a significant perturbation in the stereospecificity toward the diastereomers of (Rp)- and (Sp)-adenosine 5'-(1-thiotriphosphate) (ATP alpha S), with the Rp/Sp ratio increased from < 0.02 in wild-type to 0.37 in T23A. Detailed 31P NMR analysis indicated that the stereospecificity at the AMP site was not perturbed. These results suggest that the side chain of Thr-23 is involved in catalysis, most likely via a hydrogen bonding interaction Thr-OH...O-P alpha(ATP).(ABSTRACT TRUNCATED AT 250 WORDS)

Consequence of phosphorus stereochemistry upon the postinhibitory reaction kinetics of acetylcholinesterase poisoned by phosphorothiolates

Reaction of the chiral isomers of isoparathion methyl with solubilized rat brain cholinesterase (RBAChE) produced O,S-dimethylphosphorothiolated forms of the inhibited enzyme. The inhibited enzymes were evaluated for their individual rates of spontaeous reactivation, oxime-mediated reactivation, and non-reactivatability, and those rates were compared to those of RBAChE inhibited by the racemate

A method for chiral thiophosphonate synthesis and its use in elucidating the phosphorus stereochemistry of the hydrolytic carbon-phosphorus bond cleavage reaction of thiophosphonoacetaldehyde

A method for chiral thiophosphonate synthesis and its use in elucidating the phosphorus stereochemistry of the hydrolytic carbon-phosphorus bond cleavage reaction of thiophosphonoacetaldehyde

Use of carbohydrate derivatives for studies of phosphorus stereochemistry. Part 8. Preparation and some reactions of 1,3,2-oxazaphospholidine-2-ones and -2-thiones derived from 2-deoxy-3,4,6-tri-O-methyl-2-methylamino-D-glucopyranose

The four cyclic phosphorus esters from the reaction of MePSCl2 with 2-deoxy-3,4,6-tri-O-methyl-2-methylamino-D-glucopyranose (1) have been separated with difficulty, and structures assigned. Ring-opening of the isomers and subsequent detachment of the chiral phosphorus group from the carbohydrate moiety occurs in both acid and base, the nature of the products varying with reaction conditions and initial stereochemistry. In acid the P–N bond is broken first and then the C–O bond. In base P–N and P–O bonds are cleaved competitively; when the P–N bond is cleaved first subsequent detachment of the phosphorus group from the carbohydrate occurs by C–O and P–O bond cleavage depending on the anomeric configuration and on the concentration of the base. The P–N and P–O bond breaking reactions are highly stereoselective occurring with inversion of configuration. Reactions of (1) with PhPSCl2, MePOCl2, and PhPOCl2 and ring-opening of the resultant esters are also described.

CRYSTAL AND MOLECULAR STRUCTURE OF 2-OXO-BIS(2-β-CHLOROETHYLAMINO)-4,6-DIMETHYL-1,3,2-OXAZAPHOSPHORINANE: AN ANALOGUE OF CYCLOPHOSPHAMIDE

Abstract The isomer of the title compound chosen for determination of its crystal and molecular structure by x-ray means has been found to possess an axial mustard group and an equatorial phosphoryl oxygen. This contrasts the phosphorus stereochemistry in cyclophosphamide in which these groups are interchanged. As a consequence of forcing the mustard group into the axial position in the title compound, the C2N plane of this moiety is positioned such that neither of the pendant ClCH2CH2 groups are under the ring. The rotomeric conformation of this group differs from that in cyclophosphamide wherein the mustard C2N plane is perpendicular to the OPN plane in the ring.

Analogies between silicon and phosphorus stereochemistry—II : Influence of the attacking anion upon the stereochemistry of nucleophilic displacement at tetrahedral phosphorus

The stereochemistry of reactions of cyclic halogenophosphates with a representative series of p-substituted aryloxides emphasizes the relative influence of the attacking anion. For a given leaving group, the stereochemistry depends essentially upon the electronic character of the p-substituent and the ion-pair dissociation of the nucleophile. Both stereochemical and kinetic data rule out a cation-assisted mechanism to explain retention at phosphorus. Meanwhile, a comparison between S N2(P) and S N2(Si) suggests similar mechanisms in the two series. Retention and/or inversion are the consequence of two competing reactions of similar energies. The stereochemistry is determined by the factors which affect the approach of the nucleophile to give two initial intermediates of different geometries.

ChemInform Abstract: PHOSPHORUS STEREOCHEMISTRY. MECHANISTIC IMPLICATIONS OF THE OBSERVED STEREOCHEMISTRY OF BOND FORMING AND BREAKING PROCESSES AT PHOSPHORUS IN SOME 5‐ AND 6‐MEMBERED CYCLIC PHOSPHORUS ESTERS

Chemischer InformationsdienstVolume 11, Issue 45 Reviews ChemInform Abstract: PHOSPHORUS STEREOCHEMISTRY. MECHANISTIC IMPLICATIONS OF THE OBSERVED STEREOCHEMISTRY OF BOND FORMING AND BREAKING PROCESSES AT PHOSPHORUS IN SOME 5- AND 6-MEMBERED CYCLIC PHOSPHORUS ESTERS R. C. HALL, R. C. HALLSearch for more papers by this authorT. D. INCH, T. D. INCHSearch for more papers by this author R. C. HALL, R. C. HALLSearch for more papers by this authorT. D. INCH, T. D. INCHSearch for more papers by this author First published: November 11, 1980 https://doi.org/10.1002/chin.198045337Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume11, Issue45November 11, 1980 RelatedInformation

Phosphorus stereochemistry : Mechanistic implications of the observed stereochemistry of bond forming and breaking processes at phosphorus in some 5- and 6-membered cyclic phosphorus esters

The stereochemistry of endocyclic and exocyclic bond forming and breaking processes in 5- and 6-membered cyclic phosphorus esters is summarised and comparisons are made with analogous reactions in acyclic phosphorus esters. The factors that determine which bonds are broken and whether reactions occur with inversion or retention of configuration at phosphorus are complex and usually have more obvious effects for reactions in cyclic than in acyclic phosphorus esters ; in particular conformational effects may be important. The stereochemistry of migration of phosphorus ester groups across 1,3-diols is also described. It is suggested that nucleophilic substitutions at phosphorus are inherently stereospecific in the sense that trigonal bipyramidal reaction intermediates break down either directly or following a single Berry Pseudorotation or Turnstile rotation process. Multiple Turnstile rotations which would lead to racemisation, and which apparently do occur in stable phosphoranes, are insignificant for reactions involving trigonal bipyramidal intermediates.