Insights into the Allosteric Effect of SENP1 Q597A Mutation on the Hydrolytic Reaction of SUMO1 via an Integrated Computational Study

Small ubiquitin-related modifier (SUMO)-specific protease 1 (SENP1) is a cysteine protease that catalyzes the cleavage of the C-terminus of SUMO1 for the processing of SUMO precursors and deSUMOylation of target proteins. SENP1 is considered to be a promising target for the treatment of hepatocellular carcinoma (HCC) and prostate cancer. SENP1 Gln597 is located at the unstructured loop connecting the helices α4 to α5. The Q597A mutation of SENP1 allosterically disrupts the hydrolytic reaction of SUMO1 through an unknown mechanism. Here, extensive multiple replicates of microsecond molecular dynamics (MD) simulations, coupled with principal component analysis, dynamic cross-correlation analysis, community network analysis, and binding free energy calculations, were performed to elucidate the detailed mechanism. Our MD simulations showed that the Q597A mutation induced marked dynamic conformational changes in SENP1, especially in the unstructured loop connecting the helices α4 to α5 which the mutation site occupies. Moreover, the Q597A mutation caused conformational changes to catalytic Cys603 and His533 at the active site, which might impair the catalytic activity of SENP1 in processing SUMO1. Moreover, binding free energy calculations revealed that the Q597A mutation had a minor effect on the binding affinity of SUMO1 to SENP1. Together, these results may broaden our understanding of the allosteric modulation of the SENP1−SUMO1 complex.     

SENP2 regulates mitochondrial function and insulin secretion in pancreatic β cells

Increasing evidence has shown that small ubiquitin-like modifier (SUMO) modification plays an important role in metabolic regulation. We previously demonstrated that SUMO-specific protease 2 (SENP2) is involved in lipid metabolism in skeletal muscle and adipogenesis. In this study, we investigated the function of SENP2 in pancreatic β cells by generating a β cell-specific knockout (Senp2-βKO) mouse model. Glucose tolerance and insulin secretion were significantly impaired in the Senp2-βKO mice. In addition, glucose-stimulated insulin secretion (GSIS) was decreased in the islets of the Senp2-βKO mice without a significant change in insulin synthesis. Furthermore, islets of the Senp2-βKO mice exhibited enlarged mitochondria and lower oxygen consumption rates, accompanied by lower levels of S616 phosphorylated DRP1 (an active form of DRP1), a mitochondrial fission protein. Using a cell culture system of NIT-1, an islet β cell line, we found that increased SUMO2/3 conjugation to DRP1 due to SENP2 deficiency suppresses the phosphorylation of DRP1, which possibly induces mitochondrial dysfunction. In addition, SENP2 overexpression restored GSIS impairment induced by DRP1 knockdown and increased DRP1 phosphorylation. Furthermore, palmitate treatment decreased phosphorylated DRP1 and GSIS in β cells, which was rescued by SENP2 overexpression. These results suggest that SENP2 regulates mitochondrial function and insulin secretion at least in part by modulating the phosphorylation of DRP1 in pancreatic β cells.Subject terms: Sumoylation, Diabetes, Mechanisms of disease, Phosphorylation     

Total Chemical Synthesis of SUMO and SUMO‐Based Probes for Profiling the Activity of SUMO‐Specific Proteases

SUMO is a post‐translational modifier critical for cell cycle progression and genome stability that plays a role in tumorigenesis, thus rendering SUMO‐specific enzymes potential pharmacological targets. However, the systematic generation of tools for the activity profiling of SUMO‐specific enzymes has proven challenging. We developed a diversifiable synthetic platform for SUMO‐based probes by using a direct linear synthesis method, which permits N‐ and C‐terminal labelling to incorporate dyes and reactive warheads, respectively. In this manner, activity‐based probes (ABPs) for SUMO‐1, SUMO‐2, and SUMO‐3‐specific proteases were generated and validated in cells using gel‐based assays and confocal microscopy. We further expanded our toolbox with the synthesis of a K11‐linked diSUMO‐2 probe to study the proteolytic cleavage of SUMO chains. Together, these ABPs demonstrate the versatility and specificity of our synthetic SUMO platform for in vitro and in vivo characterization of the SUMO protease family.     

Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9

Conjugation of the small ubiquitin‐like modifier (SUMO) to protein substrates is an important disease‐associated posttranslational modification, although few inhibitors of this process are known. Herein, we report the discovery of an allosteric small‐molecule binding site on Ubc9, the sole SUMO E2 enzyme. An X‐ray crystallographic screen was used to identify two distinct small‐molecule fragments that bind to Ubc9 at a site distal to its catalytic cysteine. These fragments and related compounds inhibit SUMO conjugation in biochemical assays with potencies of 1.9–5.8 mm . Mechanistic and biophysical analyses, coupled with molecular dynamics simulations, point toward ligand‐induced rigidification of Ubc9 as a mechanism of inhibition.     

Release of Enzymatically Active Deubiquitinating Enzymes upon Reversible Capture by Disulfide Ubiquitin Reagents

Deubiquitinating enzymes (DUBs) catalyze the cleavage of ubiquitin from target proteins. Ubiquitin is post‐translationally attached to proteins and serves as an important regulatory signal for key cellular processes. In this study, novel activity‐based probes to study DUBs were synthesized that comprise a ubiquitin moiety and a novel disulfide warhead at the C‐terminus. These reagents can bind DUBs covalently by forming a disulfide bridge between the active‐site cysteine residue and the ubiquitin‐based probe. As disulfide bridges can be broken by the addition of a reducing agent, these novel ubiquitin reagents can be used to capture and subsequently release catalytically active DUBs, whereas existing capturing agents bind irreversibly. These novel reagents allow for the study of these enzymes in their active state under various conditions.     

Limiting the Number of Potential Binding Modes by Introducing Symmetry into Ligands: Structure‐Based Design of Inhibitors for Trypsin‐Like Serine Proteases

In the absence of X‐ray data, the exploration of compound binding modes continues to be a challenging task. For structure‐based design, specific features of active sites in different targets play a major role in rationalizing ligand binding characteristics. For example, dibasic compounds have been reported as potent inhibitors of various trypsin‐like serine proteases, the active sites of which contain several binding pockets that can be targeted by cationic moieties. This results in several possible orientations within the active site, complicating the binding mode prediction of such compounds by docking tools. Therefore, we introduced symmetry in bi‐ and tribasic compounds to reduce conformational space in docking calculations and to simplify binding mode selection by limiting the number of possible pocket occupations. Asymmetric bisbenzamidines were used as starting points for a multistage and structure‐guided optimization. A series of 24 final compounds with either two or three benzamidine substructures was ultimately synthesized and evaluated as inhibitors of five serine proteases, leading to potent symmetric inhibitors for the pharmaceutical drug targets matriptase, matriptase‐2, thrombin and factor Xa. This study underlines the relevance of ligand symmetry for chemical biology.     

Selective targeting of lysosomal cysteine proteases with radiolabeled electrophilic substrate analogs

BACKGROUND: The lysosomal cysteine proteases of the papain family are some of the best studied proteolytic enzymes. Small-molecule inhibitors and fluorogenic substrate mimics have been used to probe the physiological roles of these proteases. A high degree of homology between family members and overlap in substrate specificity have made elucidating individual protease function, expression and activity difficult. RESULTS: Using peptide vinyl sulfones and epoxide as templates, we have generated probes that can be tagged with radioactive iodine. The resulting compounds covalently label various cathepsins and several unidentified polypeptides likely to be proteases. MB-074 was found to be a highly selective probe of cathepsin B activity. Probes that labeled several cathepsins were used to examine the specificity and cell permeability of the CA-074 family of inhibitors. Although CA-074 reportedly acts in vivo, we find it is unable to penetrate cells. Esterifying CA-074 resulted in a cell-permeable inhibitor with dramatically reduced activity and specificity for cathepsin B. The probes were also used to monitor protease activity in primary human tumor tissue and cells derived from human placenta. CONCLUSIONS: We have generated a highly selective cathepsin B probe and several less specific reagents for the study of cathepsin biology. The reagents have several advantages over commonly used fluorogenic substrates, allowing inhibitor targets to be identified in a pool of total cellular enzymes. We have used the probes to show that cathepsin activity is regulated in tumor tissues and during differentiation of placental-derived cytotrophoblasts to invasive cells required for establishing blood circulation in a developing embryo.     

In situ selection of lead compounds by click chemistry: target-guided optimization of acetylcholinesterase inhibitors

The target-guided, in situ click chemistry approach to lead discovery has been successfully employed for discovering acetylcholinesterase (AChE) inhibitors by incubating a selected enzyme/tacrine azide combination with a variety of acetylene reagents that were not previously known to interact with the enzyme's peripheral binding site. The triazole products, formed by the enzyme, were identified by HPLC-mass spectrometry analysis of the crude reaction mixtures. The target-guided lead discovery search was also successful when performed with reagent mixtures containing up to 10 components. From 23 acetylene reagents, the enzyme selected two phenyltetrahydroisoquinoline (PIQ) building blocks that combined with the tacrine azide within the active center gorge to form multivalent inhibitors that simultaneously associate with the active and peripheral binding sites. These new inhibitors are up to 3 times as potent as our previous phenylphenanthridinium-derived compounds, and with dissociation constants as low as 33 femtomolar, they are the most potent noncovalent AChE inhibitors known. In addition, the new compounds lack a permanent positive charge and aniline groups and possess fewer fused aromatic rings. Remarkably, despite the high binding affinity, the enzyme displayed a surprisingly low preference for one PIQ enantiomer over the other.     

Mapping the Binding Site of P53 on UBC9 by NMR Spectroscopy

Human UBCP9 is a member of the E2 family of proteins.However,instead of conjugating to ubiquitin,it conjugates to a ubiquitin bomologue SUMO-1(also known as UBL1,GMP1,SMTP3,PICT-1 and sentrin).The SUMO-1 conjugation pathway is very similar to that of ubiquin with regard to the primary sequences of the ubiquitin activating enzymes(E1),the three-dimensional structures of the ubiquitin conjugating enzymes(E2),and the chemistry of the overall conjugation pathway.The interactiov of p53 and UBC9,the E2 of the SUMO-1 pathway,has heen studied by nuclear magnetic resonance spectroscopy.A peptide corresponding to the nuclear localization domain of p53 specifically interacts with UBC9 and this interaction is likely to be important for conjugation of p53 with SUMO-1.The largest chemical shift changes on UBC9 occur at residues94 and 129-135.This region is adjacent to the active site and has slgniflcant dynamic behavior on the μs-ms and ps-ns timescales.Correlation of chemical shift changes and mobility of these residues further suggest the importance of these residues in substrate recognition.     

Molecular Lamps and Molecular Golf Balls

The concave shielding of the active site of enzymes has been transferred to standard reagents of organic chemistry and concave reagents have been synthesized which possess a lamp-like geometry (concave 1,10-phenanthrolines 1–2, concave pyridines 3). The special concave geometry of these reagents is responsible for their selectivity in metal ion catalyzed (Pd-catalyzed allylations, Cu(I)-catalyzed cyclopropanations) and base catalyzed (acylation of alcohols by ketenes) reactions. For an easier recovery, these reagents have been attached to Merrifield polymers and to dendrimers. Higher generations of dendrimers loaded with concave reagents will possess a golf ball geometry.     

Oxidation-Reduction Condensation a New Method for Peptide Synthesis

Organic trivalent phosphorous compounds such as trialkyl phosphites and trialkyl or triarylphosphines are well known to be powerful deoxygenation reagents and have been used in various reduction reactions. But, it is rather a new aspect to make use of their property of deoxygenation for the gsneration of active acyl groups. Since the discovery of the rezcticn of mercuric acetate with trivalent phosphorous coqounds to yield acetic anhydride, our attention has been fccused on the generation of acyl groups and several novel reactions have been found which are applicable to the preparation of acid anhydride and peptide linkages. In considering these reactions described herein, it is necessary to choose appropriate oxidation reagents together with reducing reagents (trivalent phosphcrous compounds) because these dehydration reactions essentially proceed via an oxiaation reduction process as depicted in the following scheme.     

Studies on pyrrolidones. Synthesis and N-alkylation of β-enaminoesters derived from pyroglutamic acid

The condensation of iminoether 7 , derived from pyroglutamic acid (4) , with active methylene reagents such as Meldrum's acid or methyl cyanoacetate, lead to β-enaminoesters 2 . Solid-liquid phase transfer N-alkylation of these compounds is described.     

Resistant mechanism against nelfinavir of human immunodeficiency virus type 1 proteases

Inhibitors against human immunodeficiency virus type-1 (HIV-1) proteases are finely effective for anti-HIV-1 treatments. However, the therapeutic efficacy is reduced by the rapid emergence of inhibitor-resistant variants of the protease. Among patients who failed in the inhibitor nelfinavir (NFV) treatment, D30N, N88D, and L90M mutations of HIV-1 protease are often observed. Despite the serious clinical problem, it is not clear how these mutations, especially nonactive site mutations N88D and L90M, affect the affinity of NFV or why they cause the resistance to NFV. In this study, we executed molecular dynamics simulations of the NFV-bound proteases in the wild-type and D30N, N88D, D30N/N88D, and L90M mutants. Our simulations clarified the conformational change at the active site of the protease and the change of the affinity with NFV for all of these mutations, even though the 88th and 90th residues are not located in the NFV-bound cavity and not able to directly interact with NFV. D30N mutation causes the disappearance of the hydrogen bond between the m-phenol group of NFV and the 30th residue. N88D mutation alters the active site conformation slightly and induces a favorable hydrophobic contact. L90M mutation dramatically changes the conformation at the flap region and leads to an unfavorable distortion of the binding pocket of the protease, although 90M is largely far apart from the flap region. Furthermore, the changes of binding energies of the mutants from the wild-type protease are shown to be correlated with the mutant resistivity previously reported by the phenotypic experiments.     

Synthesis,antiproliferative activity,and molecular docking of some N-heterocycles bearing a pyrazole scaffold against liver and breast tumors

A new series of some 1,3-diphenylpyrazole-based heterocycles were constructed from 2-cyano-3-(1,3-diphenyl-1H-pyrazol-4-yl)propenoyl chloride (1) . The titled acid chloride was submitted to react with mono-nucleophilic reagents, including oxygen, sulfur, or nitrogen, to afford new acrylate, thioacrylate, and acrylamide derivatives, respectively. Meanwhile, condensation of 1 with some 1,2- and 1,3-binucleophiles led to the construction of oxadiazepine, pyridopyrimidine, and thiadiazolopyrimidine derivatives (16, 18, 20, 23) . In turn, two benzoxazinone derivatives (27, 28) were synthesized upon treating 1 with substituted anthranilic acids followed by heating with acetic anhydride. The antiproliferative activity of the compounds developed against two tumors (HePG2 and MCF7) was evaluated. Compounds 4, 6, 11, 25, and 26 exhibited strong activity and compounds 3, 5, 16, 18, 27 , and 28 exhibited moderate activity. A molecular modeling study was conducted by utilizing molecular modeling environment to test the binding free energies of the studied compounds toward human cyclin-dependent kinase 2. The compounds, 4 , 25 , and 26, displayed the best docking score. The orientation and hydrogen bond pattern of these compounds in the active site correspond to that of PNU-292137, which had been approved as a selective CDK2 inhibitor.     

Syntheses and reactivities of non-symmetrical "active ester" bi-dentate cross-linking reagents having a phthalimidoyl and acid chloride, 2-benzothiazole, or 1-benzotriazole group

We have newly synthesized the non-symmetrical "phthalimidoyl active ester" bi-dentate cross-linking reagents having an acid chloride, 2-benzothiazole, or 1-benzotriazole group (i.e., 9, 15, and 16) on the basis of the reactivity study of the "active ester" model compounds, 11-14, toward the various nucleophiles and examined their reaction selectivity towards the same nucleophiles. Then, we applied for the modification of cholesterol at the more reactive site of the bi-dentate linkers to give 3β-cholesteryl 4-(phthalimidoyloxycarbonyl)butyrate (39), and the subsequent reaction of 39 with several amines, such as benzylamine, 4-chlorobenzylamine, 2-phenylethylamine, L-phenylalanine methyl ester, or diphenylalanine benzyl ester as a protein model of the cholesterol antigen.     

Studies on Bioactive Selenium-containing Organophosphorus Compounds: Synthesis of 1-Aminoalkanephosphonate Derivatives of Benzisoselenazolone and Their Antitumor Activity

Various selenium-containing compounds are widely used as reagents and intermediates in organic synthesis.¹ In recent years biologically active organoselenium compounds have begun to attract considerable interest due to their unique and diverse potential pharmacological importance such as broad spectrum antitumor and antiviral activities, and some of them are even many times more active than their thio analogues.^2,3 It was found that benzisoselenazolones[e.g.,Ebselen, 2-phenyl-1,2-benzisoselenazol-3(2H)-one], are effective for the treatment of diseases caused by cell damage owing to increased formation of active oxygen metabolites⁴ and these pharmacological effects are mainly attributed to the glutathione peroxidase (GSH-Px) like properties.⁵     

Synthesis of Pyrimidine and Pyran Derivatives with the Related Systems and the Study of Their Behavior in the Liquid Solutions

This study aims to synthesis of condensed and non‐condensed heterocyclic rings with long fatty chains as surface active biological compounds. 2‐Cyano‐3‐(dimethylamino)‐N‐octadecylacrylamide ( 5 ) was used to synthesize pyrimidine, pyran, and other condensed products by interacting with appropriate chemical reagents. These compounds were transferred to nonionic surface‐active agents by condensation with propylene oxide. The surface and biological properties showed that these compounds have a high solubility that helps them in easy absorption and adsorption with other compounds. In addition, they have a high ability to decrease the surface tension of the liquids, good wetting, and emulsification power, which can be used at different temperatures without losing their surface or biological properties and enable them for use in industrial and pharmaceutical purposes easily.