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Biomedical subjects

Babak Borhan

Publications and source records attributed to Babak Borhan.

14 recordsLinked to original sources
PubMed2026

Influence of protein aggregates, extracellular vesicles, and lipoprotein fusion on ionizable lipid nanoparticles protein corona analysis.

Since 2018, ionizable lipid nanoparticles (LNPs) have revolutionized nucleic acid therapeutics. However, achieving potent extrahepatic delivery remains a formidable challenge, primarily due to rapid hepatic uptake driven by apolipoprotein adsorption. While analyzing the LNP protein corona is essential for engineering organ-specific tropism, these soft materials present unique analytical hurdles. Co-isolation of blood-borne contaminants, such as extracellular vesicles and lipoproteins, often masks the true corona composition. This perspective examines the critical need for refined proteomic strategies to distinguish genuine corona proteins from impurities. We propose tailored investigative approaches, suggesting the LNP protein corona significantly differs from the rigid shells observed on inorganic nanoparticles.

Nanoparticles↗
PubMed2006

The structure of Apo-wild-type cellular retinoic acid binding protein II at 1.4 A and its relationship to ligand binding and nuclear translocation.

CRABPII is a small, cytosolic protein that solubilizes and transfers retinoic acid (RA) to the nucleus while also enhancing its transcriptional activity. We have determined the first high-resolution structure of apo-wild type (WT) CRABPII at 1.35 A. Using three different data sets collected on apo-WT CRABPII we have shown that apo- and holo-CRABPII share very similar structures. Binding of RA appears to increase the overall rigidity of the structure, although the induced structural changes are not as pronounced as previously thought. The enhanced structural rigidity may be an important determinant for the enhanced nuclear localization of the RA-bound protein. Comparison of our apo-WT with a mutant apo-CRABPII structure shows that mutation of Arg111, a conserved residue of CRABPII and a key residue in RA binding, causes structural changes in the molecule. We further investigated the structural importance of conserved residues by determining the structure of the F15W mutant CRABPII (F15W-CRABPII). Our structures also demonstrate structural changes induced by crystal packing and show that a crystal can harbor demonstrative structural differences in the asymmetric unit.

Active Transport, Cell Nucleus↗
PubMed2006

Engineering a rhodopsin protein mimic.

Due to the difficulties in handling and manipulating membrane-bound proteins, such as rhodopsin, and the lack of crystallographic information on the cone opsins, we have opted to engineer a protein mimic of the transmembrane G-protein coupled receptor. Human cellular retinoic acid binding protein (CRABPII), a well studied and characterized protein, has been reengineered into a protein that now will bind retinal as a protonated Schiff base with high binding affinity (Kd = 2 nM) mimicking that of rhodopsin.

Binding Sites↗
PubMed2006

Synthesis of the proposed structure of mucoxin via regio- and stereoselective tetrahydrofuran ring-forming strategies.

An enantioselective total synthesis of the proposed structure of mucoxin (1) is described. Mucoxin, an annonaceous acetogenin isolated from bioactive leaf extracts of Rollinia mucosa, is the first acetogenin containing a hydroxylated trisubstituted tetrahydrofuran (THF) ring. This natural product is a highly potent and specific antitumor agent against MCF-7 (breast carcinoma) cell lines (ED50 = 3.7 x 10(-3) microg/mL compared to adriamycin, ED50 = 1.0 x 10(-2) microg/mL). The total synthesis described herein features two regio- and stereoselective THF ring-forming reactions. The 2,3,5-trisubstituted THF portion (C13-C17) was accessed using a highly regioselective cyclization of a methylene-interrupted epoxydiol, and the 2,5-disubstituted THF ring (C8-C12) was conveniently assembled via a 1,2-n-triol cyclization strategy. The spectral data of the synthetic material and two of its diastereomers did not match the reported data for the natural product. On the basis of detailed spectroscopic analysis of the synthesized molecule, we reason that the spectral discrepancies are due to stereochemical misassignment of the natural product.

Acetogenins↗
PubMed2006

Circular dichroism of heterochromophoric and partially regenerated purple membrane: search for exciton coupling.

In order to determine the origin of the bisignate CD spectra of native purple membrane, heterochromophoric analogues containing bacteriorhodopsin regenerated with native all-trans-retinal and retinal analogues were investigated. The data collected for the purple membrane samples containing two different chromophores suggest the additive character of the CD spectra. This conclusion was supported by a series of spectra using 5,6-dihydroretinal and 3-dehydroretinal and by using 33% regenerated PM in buffer and in presence of osmolytes. Our results support the idea of conformational heterogeneity of the chromophores in the bR in the trimer, suggesting that the three bR subunits in the trimer are not conformationally equal, and therefore, the bisignate CD spectrum of bR in the purple membrane occurs rather due to a superposition of the CD spectra from variously distorted bR subunits in the trimer than interchromophoric exciton-coupling interactions.

Bacteriorhodopsins↗
PubMed2005

Defining the retinoid binding site in the rod cyclic nucleotide-gated channel.

Rod vision is initiated when 11-cis-retinal, bound within rhodopsin, absorbs a photon and isomerizes to all-trans-retinal (ATR). This triggers an enzyme cascade that lowers cGMP, thereby closing cyclic nucleotide-gated (CNG) channels. ATR then dissociates from rhodopsin, with bright light releasing millimolar levels of ATR. We have recently shown that ATR is a potent closed-state inhibitor of the rod CNG channel, and that it requires access to the cytosolic face of the channel (McCabe, S.L., D.M. Pelosi, M. Tetreault, A. Miri, W. Nguitragool, P. Kovithvathanaphong, R. Mahajan, and A.L. Zimmerman. 2004. J. Gen. Physiol. 123:521-531). However, the details of the interaction between the channel and ATR have not been resolved. Here, we explore the nature of this interaction by taking advantage of specific retinoids and retinoid analogues, namely, beta-ionone, all-trans-C15 aldehyde, all-trans-C17 aldehyde, all-trans-C22 aldehyde, all-trans-retinol, all-trans-retinoic acid, and all-trans-retinylidene-n-butylamine. These retinoids differ in polyene chain length, chemical functionality, and charge. Results obtained from patch clamp and NMR studies have allowed us to better define the characteristics of the site of retinoid-channel interaction. We propose that the cytoplasmic face of the channel contains a retinoid binding site. This binding site likely contains a hydrophobic region that allows the ionone ring and polyene tail to sit in an optimal position to promote interaction of the terminal functional group with residues approximately 15 A away from the ionone ring. Based on our functional data with retinoids possessing either a positive or a negative charge, we speculate that these amino acid residues may be polar and/or aromatic.

Animals↗
PubMed2005

One-pot regio- and stereoselective cyclization of 1,2,n-triols.

A simple and efficient process to cyclize triols containing a 1,2-diol functionality with a pendant hydroxyl group is presented. The one-pot procedure converts the 1,2-diol into an ortho ester in situ, which upon treatment with a Lewis acid generates a cyclic acetoxonium intermediate. This intermediate is subsequently trapped by the pendant hydroxyl group to generate a cyclic ether. The stereochemistry of the 1,2-diol is transferred to the product with complete fidelity (inversion at the site of cyclization), and the reaction proceeds with high regioselectivity. The process is akin to the Lewis acid-catalyzed intramolecular ring-opening of epoxides with hydroxyl groups yielding cyclic ethers of various sizes with regio- and stereochemical control.

Journal Article↗
PubMed2004

Direct oxidative cleavage of alpha- and beta-dicarbonyls and alpha-hydroxyketones to diesters with KHSO5.

Presented is a methodology to oxidatively cleave alpha-hydroxyketones and alpha- or beta-diones using the environmentally benign reagent KHSO(5), prepared easily from Oxone, to diesters in one simple transformation. In addition, we undertook a mechanistic study to provide a plausible mechanistic interpretation. These reactions may prove to be valuable alternatives to other related metal-mediated processes.

Journal Article↗
PubMed2004

Synthesis of diastereomerically and enantiomerically pure 2,3-disubstituted tetrahydrofurans using a sulfoxonium ylide.

Nucleophilic substitution reactions of 2,3-epoxy alcohols, easily prepared via Sharpless asymmetric epoxidation chemistry, offer access to a wide variety of enantiomerically pure compounds. In this communication, we describe the use of a Payne rearrangement to control regioselectivity in the ring-opening of a series of 2,3-epoxy alcohols with dimethylsulfoxonium methylide to yield diastereomerically and/or enantiomerically pure disubstituted tetrahydrofuran rings. The factors influencing the success and substitution pattern of the THF ring products are discussed, including steric, electronic, and solvent effects.

Journal Article↗
PubMed2003

Direct lactonization of alkenols via osmium tetroxide-mediated oxidative cleavage.

[reaction: see text] A highly efficient, mild, and simple protocol is presented for the tandem OsO(4)-mediated oxidative cleavage/oxidative lactonization of alkenols to lactones. The protocol couples the OsO(4)-catalyzed oxidative cleavage of olefins with Oxone as the co-oxidant with the direct oxidation of aldehydes in alcoholic solvents to their corresponding esters.

Journal Article↗
PubMed2003

Facile oxidation of aldehydes to acids and esters with Oxone.

[reaction: see text] A highly efficient, mild, and simple protocol is presented for the oxidation of aldehydes to carboxylic acids utilizing Oxone as the sole oxidant. Direct conversion of aldehydes in alcoholic solvents to their corresponding ester products is also reported. These reactions may prove to be valuable alternatives to traditional metal-mediated oxidations.

Journal Article↗
PubMed2002

Absolute stereochemical determination of chiral carboxylic acids.

Monoamidation of 1,4-diaminobenzene with alpha-chiral carboxylic acids leads to a carrier strategy for absolute stereochemical determination with bis-zinc porphyrin tweezers by exciton-coupled circular dichroism (ECCD). The helicity induced in the porphyrin tweezers upon complexation with the derivatized carrier originates from the preferred conformation of the C(carbonyl)-C(chiral) bond. Correct ECCD signs can be predicted by the rotamer that places the large group perpendicular to the carbonyl group with the small group facing the porphyrin. [reaction: see text]

Journal Article↗
PubMed2002

Osmium tetroxide-promoted catalytic oxidative cleavage of olefins: an organometallic ozonolysis.

A mild, organometallic alternative to ozonolysis utilizing oxone and OsO(4) is presented. This is a direct oxidation of olefins via the carbon-carbon cleavage of an osmate ester by the action of oxone. Twenty-four different olefins were converted to their corresponding ketones or carboxylic acids in high yields (>80%). Free alcohols, acetate- and benzyl-protected alcohols, and 1,2-diols were stable under these conditions. This method should be applicable for traditional organic synthesis.

Journal Article↗