Isosteric Substitutions Research Articles

Aldose Reductase Evaluation against Diabetic Complications Using ADME and Molecular Docking Studies and DFT Calculations of Spiroindoline Derivative Molecule

In this study, the target molecule ethyl-2-(5-nitro-5'-(4-nitrophenyl)-2-oxo-3'H-spiro[indoline-3,2'-[1,3,4]oxadiazol]-1-yl)acetate, which is a spiroindoline derivative, were performed NBO analysis, molecular electrostatic potential surface (MEPS), nonlinear optics (NLO), HOMO-LUMO energy calculations, optimized molecular geometry, and mulliken atomic charges using B3LYP/B3PW91 basis set and 6-311G(d,p) approximations. Calculated results were reported. Density Functional Theory (DFT) computations were utilized to research the molecule theoretically. Moreover, molecular docking analysis of the tested compound, a spiroindoline derivative molecule targeting aldose reductase against diabetic complications, was performed using molecular docking to determine the structure-activity connection. The molecular docking study provided important information worth considering for further research. A notable outcome of bioisosteric and isosteric substitutions is the alteration in lipophilic character, an impressive characteristic in several aspects. Thus, utilizing SwissADME, lipophilic character assessments were performed for the concerned compounds.

Efficient carbon-neutral cycle reactions catalyzed by N-substituted biomimetic [Ru–Ru]-Based H-clusters

Herein, we report two biomimetic [Ru–Ru] analogs (Ru2ADTX(CO)6, X = Ts or Cbz), which contain the N-substituted azadithiolate (ADT) moiety of the native H-cluster, and their differential reactivity to the formic acid/carbon dioxide-hydrogen (FA/CO2–H2) “carbon-neutral cycle” reaction. The results show that the strongly electron-withdrawing tosyl-substituted Ru2ADTTs(CO)6 (1) exhibits a higher preference for CO2 hydrogenation, while the donor-inductive carboxybenzyl-substituted Ru2ADTCbz(CO)6 (2) favors FA dehydrogenation, supporting electronically- or sterically-substituted pendant amine bases in influencing the entry and exit of protons from the Ru–Ru active site and subsequent H2 oxidation and generation. Furthermore, the propensity of TEA in FA dehydrogenation and DBU in CO2 hydrogenation support the role of bases as sacrificial electron donors and co-reagents, respectively. In the CO2 hydrogenation reaction, the P-ligands with more phosphorus atoms exhibited higher reactivity and final CO2 conversion efficiency, indicating that the number of phosphorus atoms and the different electronic but isosteric substitutions on the P-ligands have significant effects on the reactivity of metal complexes. These results support the combination of the FA dehydrogenation of complex 2 and the CO2 hydrogenation capability of complex 1 to construct an efficient FA/CO2–H2 reversible reaction for a sustainable supply of energy and environmental CO2 control.

Topological analyses of the L-lysine exporter LysO reveal a critical role for a conserved pair of intramembrane solvent-exposed acidic residues

LysO, a prototypical member of the LysO family, mediates export of L-lysine (Lys) and resistance to the toxic Lys antimetabolite, L-thialysine (Thl) in Escherichia coli. Here, we have addressed unknown aspects of LysO function pertaining to its membrane topology and the mechanism by which it mediates Lys/Thl export. Using substituted cysteine (Cys) accessibility, here we delineated the membrane topology of LysO. Our studies support a model in which both the N- and C-termini of LysO are present at the periplasmic face of the membrane with a transmembrane (TM) domain comprising eight TM segments (TMSs) between them. In addition, a feature of intramembrane solvent exposure in LysO is inferred with the identification of membrane-located solvent-exposed Cys residues. Isosteric substitutions of a pair of conserved acidic residues, one E233, located in the solvent-exposed TMS7 and the other D261, in a solvent-exposed intramembrane segment located between TMS7 and TMS8, abolished LysO function in vivo. Thl, but not Lys, elicited proton release in inside-out membrane vesicles, a process requiring the presence of both E233 and D261. We postulate that Thl may be exported in antiport with H+ and that Lys may be a low-affinity export substrate. Our findings are compatible with a physiological scenario wherein in vivo LysO exports the naturally occurring antimetabolite Thl with higher affinity over the essential cellular metabolite Lys, thus affording protection from Thl toxicity and limiting wasteful export of Lys.

Synthesis and biological evaluation of an antibacterial azaborine retinoid isostere

Our continued synthetic interest in this class of retinoids, CD437 and its analogs, against methicillin-resistant Staphylococcus aureus (MRSA) has brought us to explore further isosteric substitutions within the scaffold. Although our previous findings have shown promising activity against gram-positive pathogens, their therapeutic viability remained an issue. Specifically, through preliminary analysis, our best performing compound, analog 2, displayed low solubility within serum as well as high affinity for retinoid binding proteins with a concentration dependent relationship. To circumvent this issue, we proposed a class of analogs containing an azaborine substitution in place of the naphthalene moiety. Azaborines have a nitrogen-boron bond substituting a carbon–carbon double bond that alters the electronics of the parent scaffold. This motif has been explored successfully in cancer research but to the best of our knowledge has yet to be applied to antibiotics. Herein, we describe the synthesis of the desired analogs, antimicrobial activity, and surprising physiochemical properties.

Solid Phase Synthesis of Sulfonimidamide Pseudopeptides and Library Generation

Many synthetic routes have been explored to make small molecule sulfonimidamides (SIAs), however, its introduction into larger molecules such as oligopeptides has not been studied before. We herein demonstrate three alternative and complementary methods for synthesis of SIA based pseudopeptides, on solid phase, using both on and off‐resin SIA‐synthesis, via sulfonimidoyl chlorides from sulfonamides, in high conversion. Beside evaluation of various resins such as 2‐CTC, Wang, and Rink amide‐ChemMatrix, the possibilities to further N‐functionalize and cyclize the SIA functionality on solid support are shown. The diastereomers of SIA containing pseudopeptides could in most cases be separated using normal reverse phase preparative HPLC. The solid phase SIA methodology has many advantages when it comes to handling and purification as compared to in solution, and will therefore enable exploration of the SIA group as isosteric substitutions and peptidomimetic building blocks in the development of drug‐like pseudopeptides in many ways. Of particular note these approaches facilitate combinatorial library synthesis as demonstrated herein.

Scaffold hopping and optimisation of 3’,4’-dihydroxyphenyl- containing thienopyrimidinones: synthesis of quinazolinone derivatives as novel allosteric inhibitors of HIV-1 reverse transcriptase-associated ribonuclease H

Bioisosteric replacement and scaffold hopping are powerful strategies in drug design useful for rationally modifying a hit compound towards novel lead therapeutic agents. Recently, we reported a series of thienopyrimidinones that compromise dynamics at the p66/p51 HIV-1 reverse transcriptase (RT)-associated Ribonuclease H (RNase H) dimer interface, thereby allosterically interrupting catalysis by altering the active site geometry. Although they exhibited good submicromolar activity, the isosteric replacement of the thiophene ring, a potential toxicophore, is warranted. Thus, in this article, the most active 2-(3,4-dihydroxyphenyl)-5,6-dimethylthieno[2,3-d]pyrimidin-4(3H)-one 1 was selected as the hit scaffold and several isosteric substitutions of the thiophene ring were performed. A novel series of highly active RNase H allosteric quinazolinone inhibitors was thus obtained. To determine their target selectivity, they were tested against RT-associated RNA-dependent DNA polymerase (RDDP) and integrase (IN). Interestingly, none of the compounds were particularly active on (RDDP) but many displayed micromolar to submicromolar activity against IN.

Aromaticity of unsaturated BEC4 heterocycles (E = N, P, As, Sb, O, S, Se, Te)

A compendium of pnictogen and chalcogen substituted boron heterocycles were assessed for their aromatic character by first principles density functional theory. Group-15 and Group-16 elements were placed at the ortho-, meta-, and para-positions of six-membered rings relative to boron to assess their impact on the aromaticity of the unsaturated heterocycles. Aromaticity was analyzed by a multidimensional approach using nuclear independent chemical shifts, gauge-including magnetically induced current, as well as natural bond orbital and natural resonance theory analyses. Based on these methods, we observe a general decline of aromaticity in heavier pnictaborines while the chalcogen analogues maintain relatively strong aromatic character. These general trends result from complementary π-π* natural bond order interactions that sustain resonance within the ring of each heterocycle establishing a pattern of cyclic delocalization. Consequently, natural resonance theory displays strong resonance, which is corroborated with the signed modulus of ring current, toroidal vortices of current maps, and elevated average induced current throughout the ring. The 1,3-configurations for pnictaborines and chalcogenaborines are generally more aromatic compared to the 1,2- and 1,4-isomers, which contain π-holes that limit diatropism within the heterocycles. However, an energetic trend favors the 1,2-heterocycles in both groups, with a few exceptions driven in large-part by π-donation of the lone pair on the heteroatom to the pz orbital on the adjacent boron resulting in stabilization. The importance of planarity for high aromaticity is demonstrated, especially in the pnictaborine isomers where pyramidalization at the pnictogen is favored, while bond regularity seems a less important criterion.

Effects of isosteric substitutions on the conformational preference and cis–trans isomerization of proline-containing peptides

Isosteric substitutions of the peptide CO group by CS and CSe groups increased thetranspopulation and rotational barrier to the prolylcis–transisomerization of proline-containing peptides.

From pyrrolidinyl-benzodioxane to pyrrolidinyl-pyridodioxanes, or from unselective antagonism to selective partial agonism at α4β2 nicotinic acetylcholine receptor

Each of the four aromatic –CH= of (S,R)-2-pyrrolidinyl-1,4-benzodioxane [(S,R)-6] and of its epimer at the dioxane stereocenter (S,S)-6, previously reported as α4β2 nAChR ligands, was replaced with nitrogen. The resulting four diastereoisomeric pairs of pyrrolidinyl-pyridodioxanes were studied for the nicotinic affinity and activity at α4β2, α3β4 and α7 nAChR subtypes and compared to their common carbaisostere. It turned out that such isosteric substitutions are highly detrimental, but with the important exception of the S,R stereoisomer of the pyrrolidinyl-pyridodioxane with the pyridine nitrogen adjacent to the dioxane and seven atoms distant from the pyrrolidine nitrogen. Indeed, this stereo/regioisomer not only maintained the α4β2 affinity of [(S,R)-6], but also greatly improved in selectivity over the α3β4 and α7 subtypes and, most importantly, exhibited a highly selective α4β2 partial agonism. The finding that [(S,R)-6] is, instead, an unselective α4β2 antagonist indicates that the benzodioxane substructure confers affinity for the α4β2 nAChR binding site, but activation of this receptor subtype needs benzodioxane functionalization under strict steric requirements, such as the previously reported 7-OH substitution or the present isosteric modification.

Role of Cross-Cleft Contacts in NMDA Receptor Gating

In response to brief glutamate exposure, NMDA receptors produce excitatory currents that have sub-maximal amplitudes and characteristically slow kinetics. The activation sequence starts when glutamate binds to residues located on the upper lobe of extracellularly located ligand-binding domains (LBDs) and then contacts lower lobe residues to bridge the cleft between the two hinged lobes. This event stabilizes a narrow-cleft LBD conformation and may facilitate subsequent inter-lobe contacts that further stabilize the closed cleft. Agonist efficacy has been traced to the degree of agonist-induced cleft-closure and may also depend on the stability of the closed-cleft conformation. To investigate how cross-cleft contacts contribute to the amplitude and kinetics of NMDA receptor response, we examined the activation reaction of GluN1/GluN2A receptors that had single-residue substitutions at the interface between LBD lobes. We found that side-chain truncations at residues of putative contact between lobes increased glutamate efficacy through independent additive mechanisms in GluN1 and GluN2A subunits. In contrast, removing side-chain charge with isosteric substitutions at the same sites decreased glutamate efficacy. These results support the view that in GluN1/GluN2A receptors’ natural interactions between residues on opposing sides of the ligand-binding cleft encode the stability of the glutamate-bound closed-cleft conformations and limit the degree of cleft closure, thus contributing to the sub-maximal response and emblematically slow NMDA receptor deactivation after brief stimulation.

Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop.

The sarcin-ricin RNA motif (SR motif) is one of the most prominent recurrent RNA building blocks that occurs in many different RNA contexts and folds autonomously, that is, in a context-independent manner. In this study, we combined bioinformatics analysis with explicit-solvent molecular dynamics (MD) simulations to better understand the relation between the RNA sequence and the evolutionary patterns of the SR motif. A SHAPE probing experiment was also performed to confirm the fidelity of the MD simulations. We identified 57 instances of the SR motif in a nonredundant subset of the RNA X-ray structure database and analyzed their base pairing, base-phosphate, and backbone-backbone interactions. We extracted sequences aligned to these instances from large rRNA alignments to determine the frequency of occurrence for different sequence variants. We then used a simple scoring scheme based on isostericity to suggest 10 sequence variants with a highly variable expected degree of compatibility with the SR motif 3D structure. We carried out MD simulations of SR motifs with these base substitutions. Nonisosteric base substitutions led to unstable structures, but so did isosteric substitutions which were unable to make key base-phosphate interactions. The MD technique explains why some potentially isosteric SR motifs are not realized during evolution. We also found that the inability to form stable cWW geometry is an important factor in the case of the first base pair of the flexible region of the SR motif. A comparison of structural, bioinformatics, SHAPE probing, and MD simulation data reveals that explicit solvent MD simulations neatly reflect the viability of different sequence variants of the SR motif. Thus, MD simulations can efficiently complement bioinformatics tools in studies of conservation patterns of RNA motifs and provide atomistic insight into the role of their different signature interactions.

Designing Multitarget Anti‐inflammatory Agents: Chemical Modulation of the Lumiracoxib Structure toward Dual Thromboxane Antagonists–COX‐2 Inhibitors

A series of lumiracoxib derivatives were designed to explore the influence of isosteric substitution on balancing COX-2 inhibition and thromboxane A(2) prostanoid (TP) receptor antagonism. The compounds were synthesized through a copper-catalyzed coupling procedure and characterized for their pK(a) values. TP receptor antagonism was assessed on human platelets; COX-2 inhibition was determined on human isolated monocytes and human whole blood. TPα receptor binding of the most promising compounds was evaluated through radioligand binding assays. Some of the isosteric substitutions at the carboxylic acid group afforded compounds with improved TP receptor antagonism; of these, a tetrazole derivative retained good COX-2 inhibitory activity and selectivity. The identification of this tetrazole acting as a balanced dual-acting compound in human whole blood, along with SAR analysis of the synthesized lumiracoxib derivatives, might contribute to the rational design of a new class of cardioprotective anti-inflammatory agents.

FK228 Analogues Induce Fetal Hemoglobin in Human Erythroid Progenitors

Fetal hemoglobin (HbF) improves the clinical severity of sickle cell disease (SCD), therefore, research to identify HbF-inducing agents for treatment purposes is desirable. The focus of our study is to investigate the ability of FK228 analogues to induce HbF using a novel KU812 dual-luciferase reporter system. Molecular modeling studies showed that the structure of twenty FK228 analogues with isosteric substitutions did not disturb the global structure of the molecule. Using the dual-luciferase system, a subgroup of FK228 analogues was shown to be inducers of HbF at nanomolar concentrations. To determine the physiological relevance of these compounds, studies in primary erythroid progenitors confirmed that JMA26 and JMA33 activated HbF synthesis at levels comparable to FK228 with low cellular toxicity. These data support our lead compounds as potential therapeutic agents for further development in the treatment of SCD.

Efficient Solid-Phase Synthesis of FK228 Analogues as Potent Antitumoral Agents

Novel structural analogues of a HDAC inhibitor FK228 have been synthesized by modifying the most synthetically challenging unit, (3 S,4 E)-3-hydroxy-7-mercaptoheptenoic acid, with simple isosteric substitutions. These changes did not alter the backbone structure from FK228 but enabled facile and rapid synthesis by using readily available starting materials and high-yielding reactions. FK228 analogues were examined for their antitumoral activity on a variety of human cancer cells and led to the identification of new potent compounds.

Effect of Thioxopeptide Bonds on α-Helix Structure and Stability

Thioxoamide (thioamide) bonds are nearly isosteric substitutions for amides but have altered hydrogen-bonding and photophysical properties. They are thus well-suited backbone modifications for physicochemical studies on peptides and proteins. The effect of thioxoamides on protein structure and stability has not been subject to detailed experimental investigations up to date. We used alanine-based model peptides to test the influence of single thioxoamide bonds on alpha-helix structure and stability. The results from circular dichroism measurements show that thioxoamides are strongly helix-destabilizing. The effect of an oxo-to-thioxoamide backbone substitution is of similar magnitude as an alanine-to-glycine substitution resulting in a helix destabilization of about 7 kJ/mol. NMR characterization of a helical peptide with a thioxopeptide bond near the N-terminus indicates that the thioxopeptide moiety is tolerated in helical structures. The thioxoamide group is engaged in an i, i+4 hydrogen bond, arguing against the formation of a 3(10)-helical structure as suggested for the N-termini of alpha-helices in general and for thioxopeptides in particular.

ISFOLD: Structure Prediction of Base Pairs in Non-Helical RNA Motifs from Isostericity Signatures in Their Sequence Alignments

The existence and identity of non-Watson-Crick base pairs (bps) within RNA bulges, internal loops, and hairpin loops cannot reliably be predicted by existing algorithms. We have developed the Isfold (Isosteric Folding) program as a tool to examine patterns of nucleotide substitutions from sequence alignments or mutation experiments and identify plausible bp interactions. We infer these interactions based on the observation that each non-Watson-Crick bp has a signature pattern of isosteric substitutions where mutations can be made that preserve the 3D structure. Isfold produces a dynamic representation of predicted bps within defined motifs in order of their probabilities. The software was developed under Windows XP, and is capable of running on PC and MAC with Matlab 7.1 (SP3) or higher. A PC standalone version that does not require Matlab also is available. This software and a user manual are freely available at www.ucsf.edu/frankel/isfold.

Selenium Analogues of Antithyroid Drugs – Recent Developments

Thyroxine (T4), the main secretory hormone of the thyroid gland, is produced on thyroglobulin by thyroid peroxidase (TPO)/H(2)O(2)/iodide system and deiodinated to its active form (T3) by a selenocysteine-containing enzyme, iodothyronine deiodinase (ID). The activation of thyroid-stimulating hormone (TSH) receptor by auto-antibodies leads to 'hyperthyroidism', a life-threatening disease which is treated by antithyroid drugs such as 6-propyl-2-thiouracil (PTU) and methimazole (MMI). The present review describes the biological activities of a number of S/Se derivatives bearing the methimazole pharmacophore. It is shown that the isosteric substitutions in the existing drugs lead to compounds that can effectively and reversibly inhibit the heme-containing lactoperoxidase (LPO). In contrast to methimazole, the selenium analogue, MSeI, does not interfere with the enzyme directly, but it inhibits LPO by reducing the H(2)O(2) that is required for the oxidation of the Fe-center in LPO. These studies reveal that the degradation of the intracellular H(2)O(2) by the Se analogues of antithyroid drugs may be beneficial to the thyroid gland, as these compounds may act as antioxidants and protect thyroid cells from oxidative damage. Because the drugs with an action essentially on H(2)O(2) can reversibly inhibit the thyroid peroxidase, such drugs could be of great importance in the treatment of hyperthyroidism.

Pressure- and temperature-induced unfolding studies: thermodynamics of core hydrophobicity and packing of ribonuclease A

In this work we demonstrate that heat and pressure induce only slightly different energetic changes in the unfolded state of RNase A. Using pressure and temperature as denaturants on a significant number of variants, and by determining the free energy of unfolding at different temperatures, we estimated the stability of variants unable to complete the unfolding transition owing to the experimental conditions required for pressure experiments. The overall set of results allowed us to map the contributions to stability of the hydrophobic core residues of RNase A, with the positions most critical for stability being V54, V57, I106 and V108. We also show that the stability differences can be attributed to both hydrophobic interactions and packing density with an equivalent energetic magnitude. The main hydrophobic core of RNase A is tightly packed, as shown by the small-to-large and isosteric substitutions. In addition, we found that large changes in the number of methylene groups have non-additive positive stability interaction energies that are consistent with exquisite tight core packing and rearrangements of van der Waals' interactions in the protein interior, even after drastic deleterious substitutions.

Non-Watson−Crick Base Pairing in RNA. Quantum Chemical Analysis of the cis Watson−Crick/Sugar Edge Base Pair Family

Large RNA molecules exhibit an astonishing variability of base-pairing patterns, while many of the RNA base-pairing families have no counterparts in DNA. The cis Watson-Crick/sugar edge (cis WC/SE) RNA base pairing is investigated by ab initio quantum chemical calculations. A detailed structural and energetic characterization of all 13 crystallographically detected members of this family is provided by means of B3LYP/6-31G and RIMP2/aug-cc-pVDZ calculations. Further, a prediction is made for the remaining 3 cis WC/SE base pairs which are yet to be seen in the experiments. The interaction energy calculations point at the key role of the 2'-OH group in stabilizing the sugar-base contact and predict all 16 cis WC/SE base-pairing patterns to be nearly isoenergetic. The perfect correlation of the main geometrical parameters in the gas-phase optimized and X-ray structures shows that the principle of isosteric substitutions in RNA is rooted from the intrinsic structural similarity of the isolated base pairs. The present quantum chemical calculations for the first time analyze base pairs involving the ribose 2'-OH group and unambiguously correlate the structural information known from experiments with the energetics of interactions. The calculations further show that the relative importance and absolute value of the dispersion energy in the cis WC/SE base pairs are enhanced compared to the standard base pairs. This may by an important factor contributing to the strength of such interactions when RNA folds in its polar environment. The calculations further demonstrate that the Cornell et al. force field commonly used in molecular modeling and simulations provides satisfactory performance for this type of RNA interactions.

The annotation of RNA motifs

The recent deluge of new RNA structures, including complete atomic-resolution views of both subunits of the ribosome, has on the one hand literally overwhelmed our individual abilities to comprehend the diversity of RNA structure, and on the other hand presented us with new opportunities for comprehensive use of RNA sequences for comparative genetic, evolutionary and phylogenetic studies. Two concepts are key to understanding RNA structure: hierarchical organization of global structure and isostericity of local interactions. Global structure changes extremely slowly, as it relies on conserved long-range tertiary interactions. Tertiary RNA–RNA and quaternary RNA–protein interactions are mediated by RNA motifs, defined as recurrent and ordered arrays of non-Watson–Crick base-pairs. A single RNA motif comprises a family of sequences, all of which can fold into the same three-dimensional structure and can mediate the same interaction(s). The chemistry and geometry of base pairing constrain the evolution of motifs in such a way that random mutations that occur within motifs are accepted or rejected insofar as they can mediate a similar ordered array of interactions. The steps involved in the analysis and annotation of RNA motifs in 3D structures are: (a) decomposition of each motif into non-Watson–Crick base-pairs; (b) geometric classification of each basepair; (c) identification of isosteric substitutions for each basepair by comparison to isostericity matrices; (d) alignment of homologous sequences using the isostericity matrices to identify corresponding positions in the crystal structure; (e) acceptance or rejection of the null hypothesis that the motif is conserved.