Molecular modeling for the interaction between proteasome beta 5 subunit and organotin compounds

It has been reported that organotins can inhibit the proteasomal chymotrypsin-like activity and induce cell death, but the interaction mode of organotins with proteasome has not been well defined. In this study, the IC₅₀ of butyltins and phenyltins against the proteasomal activity and the nature of their inhibition were investigated. It was found that both mono- and di-organotins were weak, reversible inhibitors against the proteasome, while tributyltin and triphenyltin were potent, irreversible proteasome inhibitors. In silico studies using the reversible organotin proteasome inhibitors demonstrated a tight correlation of the estimated proteasomal inhibition constants (Ki) with the experimental IC₅₀ values for proteasome inhibition. Furthermore, the Sn atom in TBT and TPT was found susceptible to form a coordinate bond with Thr 1 O^γ of the β5 subunit, which may account for the irreversible proteasome inhibition. The computational docking approach well predicted the inhibition nature of organotins toward the proteasomal chymotrypsin-like activity. This predictive model might aid in understanding the cytotoxic behavior of similar organometallic compounds.     

Design of active-site-directed fluorescent probes and their reactions with biopolymers

Fluorescent probes which are active-site-directed, reversible, competitive inhibitors of serum cholinesterase (ChE) enzymes have been designed and synthesized. Reversible inhibitors of enzyme active sites have a unique importance when they act as fluorescent probes, allowing fluorescence spectroscopic detection of conformation changes and activesite dynamics. 5-Dimethylamino-naphthalene-1-sulfonamido-N,N-dimethyl-n-propyl-amine and its aliphatic quaternary derivative are fluorescent probes for serum cholinesterase. The quaternary probe forms complexes with acetylcholinesterase (AChE). The dissociation constants K_d for the two probes with serum ChE are 6.0 × 10^?7 and 6.5 × 10^?7M. The inhibition constants K_i are 3.1 × 10^?6 and 6.3 × 10^?6M from the slopes of Lineweaver-Burk plots. The Michelis constant K_m for the enzyme was 8.8 × 10^?4M.     

Boron‐Based Drug Design

The use of the element boron, which is not generally observed in a living body, possesses a high potential for the discovery of new biological activity in pharmaceutical drug design. In this account, we describe our recent developments in boron‐based drug design, including boronic acid containing protein tyrosine kinase inhibitors, proteasome inhibitors, and tubulin polymerization inhibitors, and ortho‐carborane‐containing proteasome activators, hypoxia‐inducible factor 1 inhibitors, and topoisomerase inhibitors. Furthermore, we applied a closo‐dodecaborate as a water‐soluble moiety as well as a boron‐10 source for the design of boron carriers in boron neutron capture therapy, such as boronated porphyrins and boron lipids for a liposomal boron delivery system.     

Engineered Peptide Macrocycles Can Inhibit Matrix Metalloproteinases with High Selectivity

Matrix metalloproteinases (MMPs) are zinc‐dependent endopeptidases at the intersection of health and disease due to their involvement in processes such as tissue repair and immunity as well as cancer and inflammation. Because of the high structural conservation in the catalytic domains and shallow substrate binding sites, selective, small‐molecule inhibitors of MMPs have remained elusive. In a tour‐de‐force peptide engineering approach combining phage‐display selections, rational design of enhanced zinc chelation, and d ‐amino acid screening, we succeeded in developing a first synthetic MMP‐2 inhibitor that combines high potency (K_i=1.9±0.5 nm ), high target selectivity, and proteolytic stability, and thus fulfills all the required qualities for in cell culture and in vivo application. Our work suggests that selective MMP inhibition is achievable with peptide macrocycles and paves the way for developing specific inhibitors for application as chemical probes and potentially therapeutics.     

Structure‐Reactivity Relationships as Probes to Acetylcholinesterase Inhibition Mechanisms by Aryl Carbamates. II. Hammett‐Taft Cross‐Interaction Correlations

Substituted phenyl‐N‐butyl carbamates ( 1 ) and p‐nitrophenyl‐N‐substituted carbamates ( 2 ) are characterized as “pseudo‐pseudo‐substrate” inhibitors of acetylcholinesterase. Since the inhibitors protonate in pH 7.0 buffer solution, the virtual inhibition constants (K_i's) of the protonated inhibitors can be calculated from the equation, ‐logK_i' = ‐logK_i ‐ pK_a + 14. The ‐logK_i' and logk_c values for acetylcholinesterase inhibitions by carbamates 1 correlate with the Hammett equation (log(k/k₀) = ρσ); moreover, those by carbamates 2 correlate with the Taft equation (log(k/k₀) = ρ* σ*). With modified Hammett‐Taft cross‐interaction variations, multiple linear regressions of the ‐logK_i' and logk_c values of carbamates 1 and 2 give good correlations, and the cross‐interaction constants (ρ_XR) are 0.5 and 0.0, respectively. The ρ_XR value of 0.5 indicates that the carbamate O‐C(O)‐N‐R geometries for the transition states that lead to enzyme‐carbamate tetrahedral intermediates are all pseudo‐trans conformations. Therefore, the carbamate moiety of the inhibitors stretches along the active site gorge of the enzyme but does not bind in the acyl binding site pocket of the enzyme. Overall, the carbamate O‐C(O)‐N‐R geometries for carbamates 1 and 2 , protonated carbamates 1 and 2 , and the tetrahedral intermediate are all retained in pseudo‐trans conformations. The ρ_XR value of 0.0 suggests that the transition states that lead to the carbamyl enzymes are breaking C‐O bonds and are excluding the leaving groups, substituted phenols.     

Proteasom‐Inhibitoren

The proteasome is a multicatalytic protease complex with an unusual enzyme mechanism. It plays a central role in intracellular protein degradation and its important function in the regulation of the cell cycle makes it an interesting target for cancer therapy. First developed as reagents to elucidate the catalytic functions of the proteasome, several proteasome inhibitors are presently being tested in clinical trials. It appears that proteasome inhibitors of the classes peptidyl boronic acids, peptide epoxyketones, and β‐lactone‐γ‐lactams are particularly effective as anticancer agents.     

Aβ-binding molecules: Possible application as imaging probes and as anti-aggregation agents

As amyloid β (Aβ) is at the centre of pathogenesis of Alzheimer's disease (AD), Aβ aggregate-specific probes for in vivo studies of Aβ are potentially important for the early diagnosis and the assessment of new treatment strategies in the AD brain by noninvasive imaging. Several series of compounds derived from Congo red (CR) and Thioflavin T (ThT) have been evaluated as potential probes for the Aβ imaging. They include a diversity of core structures contributing to their affinities to Aβ. Small-molecule inhibi- tors were known to inhibit the formation of Aβ oligomers and fibrils. This inhibition has to be performed in such a way that these inhibitors bind to Aβ in the binding channel where Aβ-binding probes should sit. Therefore, several of them were used as novel core structures to develop Aβ probes, with their de- rivatives exhibiting good Aβ affinities. This approach will facilitate the design of a variety of candidates for Aβ probe molecules and anti-aggregation-therapeutic drugs. Moreover, the finding of Aβ probes with diverse core structures recognized by binding sites on Aβs will likely provide a promising per- spective for the design of 99mTc-labeled probe-derived molecules.     

Towards subunit-specific proteasome inhibitors: synthesis and evaluation of peptide alpha',beta'-epoxyketones

BACKGROUND: The proteasome is a large multicatalytic protease complex (700 kDa) involved in a number of highly regulated processes. It has three major catalytic activities: a chymotrypsin-like activity, a trypsin-like activity and a post-glutamyl peptide hydrolyzing (PGPH) activity. To be useful as molecular probes, which could help dissect the cellular functions of the proteasome, inhibitors should be specific for the proteasome, active in vivo and selectively block only one of the three catalytic activities. To date, few inhibitors fulfill these requirements so we set out to make novel proteasome inhibitors that incorporate these characteristics. RESULTS: A panel of amino-terminally acetylated peptide alpha',beta'-epoxyketones with leucine in P1 and various aliphatic or aromatic amino acids in P2-P4 were prepared and evaluated. Most compounds selectively inhibited the chymotrypsin-like activity, while only weakly inhibiting the trypsin-like and PGPH activities. After optimization, one inhibitor, Ac-hFLFL-epoxide, was found to be more potent and selective for the inhibition of the chymotrypsin-like activity than several previously described inhibitors. This inhibitor also exhibited strong in vivo anti-inflammatory activity. CONCLUSIONS: Optimization of amino-terminally acetylated peptide alpha',beta'-epoxyketones furnished a potent proteasome inhibitor, Ac-hFLFL-epoxide, that has an excellent selectivity for the chymotrypsin-like activity. The inhibitor also proved to be a potent antiproliferative and anti-inflammatory agent. The strong in vivo and in vitro activities suggest that this class of proteasome inhibitors could be both molecular probes and therapeutic agents.     

Mechanism of Copper(I)‐Catalyzed Allylic Alkylation of Phosphorothioate Esters: Influence of the Leaving Group on α Regioselectivity

The mechanism of Cu^I‐catalyzed allylic alkylation and the influence of the leaving groups (OPiv, SPiv, Cl, SPO(OiPr)₂; Piv: pivavloyl) on the regioselectivity of the reaction have been explored by using density functional theory (DFT). A comprehensive comparison of many possible reaction pathways shows that [(iPr)₂Cu]^? prefers to bind first oxidatively to the double bond of the allylic substrate at the anti position with respect to the leaving group, and this is followed by dissociation of the leaving group. If the leaving group is not taken into account, the reaction then undergoes an isomerization and a reductive elimination process to give the α‐ or γ‐selective product. If OPiv, SPiv, Cl, or SPO(OiPr)₂ groups are present, the optimal route for the formation of both α‐ and γ‐substituted products changes from the stepwise elimination to the direct process, in which the leaving group plays a stabilizing role for the reactant and destabilizes the transition state. The differences to the energy barrier for the α‐ and γ‐substituted products are 2.75 kcal mol^?1 with SPO(OiPr)₂, 2.44 kcal mol^?1 with SPiv, 2.33 kcal mol^?1 with OPiv, and 1.98 kcal mol^?1 with Cl, respectively; these values show that α regioselectivity in the allylic alkylation follows a SPO(OiPr)₂>SPiv>OPiv>Cl trend, which is in satisfactory agreement with the experimental findings. This trend mainly originates in the differences between the attractive electrostatic forces and the repelling steric interactions of the SPO(OiPr)₂, SPiv, OPiv, and Cl groups on the Cu group.     

A Set of Activity‐Based Probes to Visualize Human (Immuno)proteasome Activities

Proteasomes are therapeutic targets for various cancers and autoimmune diseases. Constitutively expressed proteasomes have three active sites, β1c, β2c, and β5c. Lymphoid tissues also express the immunoproteasome subunits β1i, β2i, and β5i. Rapid and simultaneous measurement of the activity of these catalytic subunits would assist in the discovery of new inhibitors, improve analysis of proteasome inhibitors in clinical trials, and simplify analysis of subunit expression. In this work, we present a cocktail of activity‐based probes that enables simultaneous gel‐based detection of all six catalytic human proteasome subunits. We used this cocktail to develop specific inhibitors for β1c, β2c, β5c, and β2i, to compare the active‐site specificity of clinical proteasome inhibitors, and to demonstrate that many hematologic malignancies predominantly express immunoproteasomes. Furthermore, we show that selective and complete inhibition of β5i and β1i is cytotoxic to primary cells from acute lymphocytic leukemia (ALL) patients.     

Revisiting Proteasome Inhibitors: Molecular Underpinnings of Their Development,Mechanisms of Resistance and Strategies to Overcome Anti-Cancer Drug Resistance

Proteasome inhibitors have shown relevant clinical activity in several hematological malignancies, namely in multiple myeloma and mantle cell lymphoma, improving patient outcomes such as survival and quality of life, when compared with other therapies. However, initial response to the therapy is a challenge as most patients show an innate resistance to proteasome inhibitors, and those that respond to the therapy usually develop late relapses suggesting the development of acquired resistance. The mechanisms of resistance to proteasome inhibition are still controversial and scarce in the literature. In this review, we discuss the development of proteasome inhibitors and the mechanisms of innate and acquired resistance to their activity—a major challenge in preclinical and clinical therapeutics. An improved understanding of these mechanisms is crucial to guiding the design of new and more effective drugs to tackle these devastating diseases. In addition, we provide a comprehensive overview of proteasome inhibitors used in combination with other chemotherapeutic agents, as this is a key strategy to combat resistance.     

Synthesis and Biological Evaluation of Potent Bisubstrate Inhibitors of the Enzyme Catechol O‐Methyltransferase (COMT) Lacking a Nitro Group

Inhibition of the enzyme catechol O‐methyltransferase (COMT) represents a viable strategy for regulation of the catabolism of catecholamine neurotransmitters or their precursors, and is of considerable interest in the therapy of Parkinson's disease. Herein, we report the development of a new generation of potent bisubstrate inhibitors of COMT derived from nitro‐substituted ligand 1 (K_i = 28 nM , Table 1), which achieve high biological activity despite the lack of a NO₂ substituent on the catechol moiety. Their synthesis takes advantage of a convergent approach, in which a series of functionalized catechol intermediates is prepared (Schemes 2–7) and coupled to a common adenosine‐derived allylic amine building block (Scheme 8). Biological activities of the newly synthesized inhibitors, determined by in vitro enzymatic assay and kinetic studies, clearly demonstrate that high inhibitory potency of the bisubstrate inhibitors is not correlated with the pK_a of the catechol OH groups. Aromatic residues, connected to the catechol via a biaryl‐type linkage, were found to maximally benefit from additional favorable hydrophobic interactions with the enzyme and thus to be preferred replacements of the NO₂ group in 1 . A competitive kinetic inhibition mechanism (Fig. 2) with respect to the cofactor binding site was confirmed in all cases, supporting a bisubstrate inhibition mode for inhibitors 2 – 19 .     

Phenothiazine-based chalcones as potential dual-target inhibitors toward cholinesterases (AChE,BuChE) and monoamine oxidases (MAO-A,MAO-B)

Chalcones targeting neurodegenerative diseases have been known as attractive structures in drug design and discovery. In this study, phenothiazine-based chalcones as ChEs and MAOs inhibitors were designed and synthesized via base-catalyzed Claisen-Schmidt condensation, and chemical structures of the compounds were elucidated by NMRs and HRMS. Compounds 3 and 9 showed promising inhibition potency against AChE enzyme with IC₅₀ values of 0.221 μM and 0.053 μM while compound 9 displayed remarkable inhibition potency toward MAO-B enzyme with IC₅₀ value of 0.048 μM. Compound 9 , as a dual-target inhibitor, selectively inhibited AChE and MAO-B enzymes. This promising behavior is an advantage for the compound since MAO-B and AChE inhibition have a role in Alzheimer's disease. Fused tricyclic ring systems such as phenothiazine incorporated with chalcone moiety being multitargeting ligands may help scientists for the rational design of novel lead compounds targeting neurodegenerative illnesses.     

Thiophene series. XV The effect of leaving groups on the reactivity of nitro-activated thiophene derivatives with sodium thiophenoxide

The effect of leaving groups on the reactivity of 3-X-2-nitrothiophene (1), 2-X-3-nitrothiophene (II) and 2-X-5-nitrothiophene (III) (X = Cl, Br, I, OC₆H₄NO₂(p), SO₂C₆ H₅) with sodium thiophenoxide has been examined. The results show that the reactivity ratio kIII/kII is always greater than unity and is relatively uninfluenced by changing leaving groups compared to the ratio kI/kII. The ratio kI/kII is greater or smaller than unity, according to following patterns of leaving groups Examination of the reactivity of the three series of compounds having Cl, Br, I and C₆H₄NO₂(p) as leaving groups showed the absence of an “element effect” which indicates that in the transition states of these displacement reactions there is little breaking of the bond to the group being displaced.     

Aminocyclopentitol Inhibitors of α‐L‐Fucosidases

Aminocyclopentitol analogs of α‐L ‐fucose were synthesized stereoselectively from D ‐ribose. Alkyl substituents were attached at the NH₂ group to mimic the glycosidic leaving group. The resulting (alkylamino)cyclopentitols inhibited α‐L ‐fucosidases selectively with inhibition constants in the range of K_i=10⁻⁷ M . Comparisons with stereoisomers and acyclic analogs showed that this inhibition only occurs with N‐alkyl substitution and proper configuration at the cyclopentane, as expected for transition‐state‐analog‐type inhibition. These observations were supported by molecular‐modeling comparisons between inhibitor and transition state.     

Substrate binding and sequence preference of the proteasome revealed by active-site-directed affinity probes

Background: The proteasome is a multicatalytic protease complex responsible for most cytosolic protein breakdown. The complex has several distinct proteolytic activities that are defined by the preference of each for the carboxyterminal (P1) amino acid residue. Although mutational studies in yeast have begun to define substrate specificities of individual catalytically active β subunits, little is known about the principles that govern substrate hydrolysis by the proteasome.Results: A series of tripeptide and tetrapeptide vinyl sulfones were used to study substrate binding and specificity of the proteasome. Removal of the aromatic amino-terminal cap of the potent tripeptide vinyl sulfone proteasome inhibitor 4-hydroxy-3-iodo-2-nitrophenyl-leucinyl-leucinyl-leucine vinyl sulfone resulted in the complete loss of binding and inhibition. Addition of a fourth amino acid (P4) to the tri-leucine core sequence fully restored inhibitory potency. 1251-labeled peptide vinyl sulfones were also used to examine inhibitor binding and to determine the correlation of subunit modification with inhibition of peptidase activity. Changing the amino acid in the P4 position resulted in dramatically different profiles of β-subunit modification.Conclusions: The P4 position, distal to the site of hydrolysis, is important in defining substrate processing by the proteasome. We observed direct correlations between subunit modification and inhibition of distinct proteolytic activities, allowing the assignment of activities to individual β subunits. The ability of tetrapeptides, but not tripeptide vinyl sulfones, to act as substrates for the proteasome suggests there could be a minimal length requirement for hydrolysis by the proteasome. These studies indicate that it is possible to generate inhibitors that are largely specific for individual β subunits of the proteasome by modulation of the P4 and carboxy-terminal vinyl sulfone moieties.     

A Minimal β‐Lactone Fragment for Selective β5c or β5i Proteasome Inhibitors

Broad‐spectrum proteasome inhibitors are applied as anticancer drugs, whereas selective blockage of the immunoproteasome represents a promising therapeutic rationale for autoimmune diseases. We here aimed at identifying minimal structural elements that confer β5c or β5i selectivity on proteasome inhibitors. Based on the natural product belactosin C, we synthesized two β‐lactones featuring a dimethoxybenzyl moiety and either a methylpropyl (pseudo‐isoleucin) or an isopropyl (pseudo‐valine) P1 side chain. Although the two compounds differ only by one methyl group, the isoleucine analogue is six times more potent for β5i (IC₅₀=14 nM ) than the valine counterpart. Cell culture experiments demonstrate the cell‐permeability of the compounds and X‐ray crystallography data highlight them as minimal fragments that occupy primed and non‐primed pockets of the active sites of the proteasome. Together, these results qualify β‐lactones as a promising lead‐structure motif for potent nonpeptidic proteasome inhibitors with diverse pharmaceutical applications.     

Design and synthesis of novel diamide derivatives of glycine as antihyperglycemic agents

DPP-4 inhibition is one of the most extensively explored approaches for the management of type 2 diabetes (T2D). Most DPP-4 inhibitors in the market contain a proline mimetic active pharmacophore. Herein, we report the design, synthesis, and preliminary evaluation of a series of novel diamide derivatives of glycine, devoid of the proline mimic, for the treatment of T2D. As predicted from in silico studies, the diamide derivatives of glycine exhibited comparable DPP-4 inhibition with the standard as confirmed by the preliminary in vitro studies. Compound 6b was found to be the most potent (IC₅₀ 94.82 nM) DPP-4 inhibitor among all the molecules synthesized in the series.     

Targeting a Large Active Site: Structure-Based Design of Nanomolar Inhibitors of Trypanosoma brucei Trypanothione Reductase

Trypanothione reductase (TR) plays a key role in the unique redox metabolism of trypanosomatids, the causative agents of human African trypanosomiasis (HAT), Chagas’ disease, and leishmaniases. Introduction of a new, lean propargylic vector to a known class of TR inhibitors resulted in the strongest reported competitive inhibitor of Trypanosoma (T.) brucei TR, with an inhibition constant K_i of 73 nm , which is fully selective against human glutathione reductase (hGR). The best ligands exhibited in vitro IC₅₀ values (half-maximal inhibitory concentration) against the HAT pathogen, T. brucei rhodesiense, in the mid-nanomolar range, reaching down to 50 nm. X-Ray co-crystal structures confirmed the binding mode of the ligands and revealed the presence of a HEPES buffer molecule in the large active site. Extension of the propargylic vector, guided by structure-based design, to replace the HEPES buffer molecule should give inhibitors with low nanomolar K_i and IC₅₀ values for in vivo studies.