Third generation of matrix metalloprotease inhibitors: Gain in selectivity by targeting the depth of the S1′ cavity

Following the disappointment of clinical trials with early broad-spectrum synthetic inhibitors of matrix metalloproteases (MMPs), the field is now resurging with a new focus on the development of more selective inhibitors. Compounds able to fully discriminate between different members of the MMP family are sorely needed for therapeutic applications. Chemical efforts over the past years have led to very few selective inhibitors of MMPs. The over-exploitation of the hydroxamate function, or other strong zinc-binding groups, might be responsible for this failure. By resorting to weaker zinc-chelating groups, like phosphoryl or carboxylic groups, inhibitors with improved selectivity profiles have been developed. However, the most encouraging results have been obtained with compounds that avoid targeting the zinc but gain their affinity from plunging deeper into the MMP S₁′ cavity. Analyses of the crystal structures of MMP-13 and MMP-8 complexes with such compounds provide novel insights for the design of more selective inhibitors for other members of the MMP family.     

Synthetic active site-directed inhibitors of metzincins: achievement and perspectives

The involvement of many zinc metalloproteinases belonging to the metzincin family with a variety of pathological states raises the possibility of therapeutic intervention using synthetic inhibitors with appropriate selectivity. Knowledge of the catalytic domain 3D-structures for various members of the metzincin family has been successfully exploited by chemists to develop potent synthetic inhibitors. However, despite intense efforts, very few highly selective inhibitors of metzincins have been discovered up to now. A survey of the literature suggests that the over-exploitation of the hydroxamate function as a zinc-binding group to develop inhibitors might be responsible for this situation. The use of alternative zinc-binding groups has led to more selective inhibitors, but the most encouraging results have been obtained for MMP-13 with compounds that do not incorporate zinc-binding groups in their structure. This new family of inhibitors exploits the presence of a deep S(1)(') cavity in the protease active site, a specific trait shared by many members of the metzincin family. However, to be successfully transposed to the metzincin members, this strategy will not only be able to exploit the structural detail of these S(1)(') cavities, but probably also subtle difference in their dynamics.     

Viral proteases: an emerging therapeutic target

Only a few viral diseases are presently treatable because of our limited knowledge of specific viral target molecules. An attractive class of viral molecules toward which chemotherapeutic agents could be aimed are proteases coded by some virus groups such as retro- or picornaviruses (poliomyelitis, common cold virus). The picornavirus enzymes were discovered first, and they have now been characterized by a combination of molecular-genetic and biochemical approaches. Several laboratories have expressed the picornaviral enzymes in heterologous systems and have reported proteolytic activity, as well as the high cleavage fidelity diagnostic of the viral proteases. After dealing with several technical difficulties often encountered in standard genetic engineering approaches, one viral protease is now available to us in quantity and is amendable to mutagenic procedures. The initial outcome of the mutagenesis studies has been the confirmation of our earlier work with inhibitors, which suggested a cysteine active-site class. There is a clustering of active-site residues which may be unique to these viruses. The requirement for an active-site cysteine-histidine pair in combination with detailed information on the viral cleavage sites has permitted design of selective inhibitors with attractive antiviral properties. Future goals include investigation of the structural basis for selective processing and application of the cleavage specificity to general problems in genetic engineering.     

Tricyclic Covalent Inhibitors Selectively Target Jak3 through an Active Site Thiol

The action of Janus kinases (JAKs) is required for multiple cytokine signaling pathways, and as such, JAK inhibitors hold promise for treatment of autoimmune disorders, including rheumatoid arthritis, inflammatory bowel disease, and psoriasis. However, due to high similarity in the active sites of the four members (Jak1, Jak2, Jak3, and Tyk2), developing selective inhibitors within this family is challenging. We have designed and characterized substituted, tricyclic Jak3 inhibitors that selectively avoid inhibition of the other JAKs. This is accomplished through a covalent interaction between an inhibitor containing a terminal electrophile and an active site cysteine (Cys-909). We found that these ATP competitive compounds are irreversible inhibitors of Jak3 enzyme activity in vitro. They possess high selectivity against other kinases and can potently (IC₅₀ < 100 nm) inhibit Jak3 activity in cell-based assays. These results suggest irreversible inhibitors of this class may be useful selective agents, both as tools to probe Jak3 biology and potentially as therapies for autoimmune diseases.     

Action of strong and weak nitrogenous bases on respiratory chain enzymes of mitochondria

The action of nitrogenous basis--electroneutral hydrazides (pK less than 7,50 and positive charged arylhydrazones (pK greater than 8)--on the respiratory chain enzymes and the influence of the electric charge and the size of alkoxylic group on biological activity compounds have been investigated. It has been shown that the size of alkoxylic group defines the selective action of nitrogenous basis on the enzymes of mitochondrial respiratory chain. The nitrogenous basis with a long alkoxylic group is shown to be inhibitors of NADH-dehydrogenase, their action is similar to rotenone. At the same time compounds with a short group are more effective in the inhibition of the enzymes of the initial segment in the respiratory chain mitochondria. The affinity of the organic cations of arylhydrazones to NADH-dehydrogenase is 100-1000 times higher than the affinity of electric neutral compounds.     

病毒逃避RNAi的策略

将病毒逃避RNAi策略的最新进展做一综述.RNA干扰(RNAi)是一个有效的抗病毒系统,并且病毒特异性小干扰RNA(siRNA)是非常有希望的抗病毒抑制剂.然而,许多病毒已经进化出了高超的策略来干扰siRNA和微RNA(miRNA)介导的沉默通路.深入理解病毒利用的逃避策略将为开发避免病毒逃逸的有效RNAi疗法奠定基础.     

Effect of structural modification on the inhibitory selectivity of rutaecarpine derivatives on human CYP1A1, CYP1A2, and CYP1B1

Derivatives of a CYP1A2 inhibitor rutaecarpine were synthesized to have potent and selective inhibition of human CYP1 members. Structural modelling shows a good fitting of rutaecarpine with the putative active site of human CYP1A2. Among the derivatives, 10- and 11-methoxyrutaecarpine are the most selective CYP1B1 inhibitors. 1-Methoxyrutaecarpine and 1,2-dimethoxyrutaecarpine are the most selective CYP1A2 inhibitors.     

G protein signaling and the molecular basis of antidepressant action

Over the past four decades, a variety of interventions have been used for the treatment of clinical depression and other affective disorders. Several distinct pharmacological compounds show therapeutic efficacy. There are three major classes of antidepressant drugs: monoamine oxidase inhibitors (MAOIs), selective serotonin reuptake inhibitors (SSRIs), and tricyclic compounds. There are also a variety of atypical antidepressant drugs, which defy ready classification. Finally, there is electroconvulsive therapy, ECT. All require chronic (2-3 weeks) treatment to achieve a clinical response. To date, no truly inclusive hypothesis concerning a mechanism of action for these diverse therapies has been formed. This review is intended to give an overview of research concerning G protein signaling and the molecular basis of antidepressant action. In it, the authors attempt to discuss progress that has been made in this arena as well as the possibility that some point (or points) along a G protein signaling cascade represent a molecular target for antidepressant therapy that might lead toward a unifying hypothesis for depression. This review is not designed to address the clinical studies. Furthermore, as it is a relatively short paper, citations to the literature are necessarily selective. The authors apologize in advance to authors whose work we have failed to cite.     

Crystal structure of human cathepsin V

Cathepsin V is a lysosomal cysteine protease that is expressed in the thymus, testis and corneal epithelium. We have determined the 1.6 A resolution crystal structure of human cathepsin V associated with an irreversible vinyl sulfone inhibitor. The fold of this enzyme is similar to the fold adopted by other members of the papain superfamily of cysteine proteases. This study provides a framework for understanding the structural basis for cathepsin V's activity and will aid in the design of inhibitors of this enzyme. A comparison of cathepsin V's active site with the active sites of related proteases revealed a number of differences, especially in the S2 and S3 subsites, that could be exploited in identifying specific cathepsin V inhibitors or in identifying inhibitors of other cysteine proteases that would be selective against cathepsin V.     

Micro RNA and viral infections in mammals

RNA silencing plays an important role in development through the action of micro (mi) RNAs that fine tune the expression of a large portion of the genome. But, in plants and insects, it is also a very important player in innate immune responses, especially in antiviral defense. It is now well established that the RNA silencing machinery targets plant as well as insect viruses. While the genetic basis underlying this defense mechanism in these organisms starts being elucidated, much less is known about the possible antiviral role of RNA silencing in mammals. In order to identify siRNAs coming from viruses in infected human cells, small RNAs from cells infected with RNA viruses, such as hepatitis C virus, yellow fever virus or HIV-1, were cloned and sequenced, but no virus-specific siRNAs could be detected. On the contrary, viral small RNAs were found in cells infected by the DNA virus Epstein-Barr. A closer look at these revealed that they were not siRNAs, but rather resembled miRNAs. This finding indicated that, rather than being targeted by RNA silencing, human DNA viruses seem to have evolved their own miRNAs to modulate the expression of host genes. This primary observation has been extended to other members of the herpesvirus family as well as other DNA viruses such as the polyomavirus SV40. Viral miRNAs have the potential to act both in cis to regulate expression of viral genes, or in trans on host genes. There are good indications for the cis mode of action, but the identification of cellular targets of these small viral regulators is only in its infancy.     

Designing TIMP (tissue inhibitor of metalloproteinases) variants that are selective metalloproteinase inhibitors

The tissue inhibitors of metalloproteinases (TIMPs) are endogenous inhibitors of the matrix metalloproteinases (MMPs), enzymes that play central roles in the degradation of extracellular matrix components. The balance between MMPs and TIMPs is important in the maintenance of tissues, and its disruption affects tissue homoeostasis. Four related TIMPs (TIMP-1 to TIMP-4) can each form a complex with MMPs in a 1:1 stoichiometry with high affinity, but their inhibitory activities towards different MMPs are not particularly selective. The three-dimensional structures of TIMP-MMP complexes reveal that TIMPs have an extended ridge structure that slots into the active site of MMPs. Mutation of three separate residues in the ridge, at positions 2, 4 and 68 in the amino acid sequence of the N-terminal inhibitory domain of TIMP-1 (N-TIMP-1), separately and in combination has produced N-TIMP-1 variants with higher binding affinity and specificity for individual MMPs. TIMP-3 is unique in that it inhibits not only MMPs, but also several ADAM (a disintegrin and metalloproteinase) and ADAMTS (ADAM with thrombospondin motifs) metalloproteinases. Inhibition of the latter groups of metalloproteinases, as exemplified with ADAMTS-4 (aggrecanase 1), requires additional structural elements in TIMP-3 that have not yet been identified. Knowledge of the structural basis of the inhibitory action of TIMPs will facilitate the design of selective TIMP variants for investigating the biological roles of specific MMPs and for developing therapeutic interventions for MMP-associated diseases.     

Inhibition of Janus kinases by tyrosine phosphorylation inhibitor,Tyrphostin AG-490

Janus kinases (JAKs) belong to a crucial family of tyrosine kinases, implicated in the patho-physiology of multiple cancer types, and serve as striking therapeutic targets. To date, many potent, either ATP-competitive (PTK domain) or non-ATP-competitive JAK inhibitors have been identified. Among them, Tyrphostin AG-490 (2-cyano-3-(3,4-dihydroxyphenyl)-N-(phenylmethyl)-2-propenamide) is a well-known ATP-competitive inhibitor. However, its mode of action, details of interacting residues, and induced conformational changes in JAK-specific binding sites remain elusive. Here, through comparative structure analysis, molecular docking, and molecular dynamics simulation assays, we explored comparative binding patterns of AG-490 against JAK1, JAK2, and JAK3. Our results entail noteworthy observations about the binding affinity of AG-490 by illustrating distinctive amino acid residues lying at the conserved ATP-binding domains of JAK family members. By subsequent assessment of their structural homology and conserved structural folds, we highlight intriguing prospects to design more specific and potent inhibitors for selective targeting of JAK family members. Our comparative study provides a platform for the rational design of precise and potent inhibitor for selective targeting of JAK family members.     

Auxin Transport Inhibitors: IV. EVIDENCE OF A COMMON MODE OF ACTION FOR A PROPOSED CLASS OF AUXIN TRANSPORT INHIBITORS: THE PHYTOTROPINS

The more active members of a proposed class of auxin transport inhibitors have been shown to have the ability to inhibit the active movement of auxin at concentrations where they have little effect on auxin action and no significant auxin activity. They have also been shown to give rise to characteristic biphasic dose-response curves on cress root growth. Based on these physiological similarities and other common physiological properties, it is concluded that they may achieve their effects by a common mode of action which differs from that of other known auxin transport inhibitors. It is suggested that the name "phytotropins" be given to the class of auxin transport inhibitors now defined by a similar mode of action and common chemical properties.     

Specific targeting of metzincin family members with small-molecule inhibitors: progress toward a multifarious challenge

Zn-metalloproteinases are an important class of hydrolytic enzymes that are characterized by the presence of a catalytic zinc(II) atom in their active center which is fundamental for proteolytic activity. Metzincins, a superfamily of Zn-metalloproteinases with many structural and functional commonalities among its members, are responsible for the fine tuning of key physiological functions in mammals and the deregulation of their activity is directly connected to numerous inflammatory and degenerative diseases such as arthritis or cancer. Development of small-molecule exogenous inhibitors of metzincins able to re-establish normal proteolytic activity in pathological conditions has been a field of intense research effort for many years but applications in the clinic were not always successful. One of the main reasons for this failure is the uncontrolled action of these inhibitors on target as well as anti-target metzincin family members. Current medicinal efforts have been shifted to the discovery of target-specific inhibitors that will help to improve our understanding of metzincins biological function and provide the basis for the development of safer pharmaceutical agents. This review focuses on the cases of certain medicinally important metzincins [matrix metalloproteinases (MMPs), a disintegrin and metalloproteinases (ADAMs), ADAMs with thrombospondin motifs (ADAMTSs), and procollagen C-proteinase (PCP)] and summarizes the latest advances on the discovery of inhibitors of these enzymes that display improved selectivity profiles.     

Characterization of a novel murine leukemia virus-related subgroup within mammals.

The murine leukemia virus (MuLV)-related retroviruses are one of seven genera which together constitute the family Retroviridae. They are widespread as both endogenous and exogenous agents within vertebrates and have been associated with a variety of malignancies and other disorders. We isolated and characterized 12 endogenous representatives of this genus from a number of mammalian hosts. Subsequent sequence analysis revealed that the isolated viruses cluster into two clearly distinct groups. All of the exogenous MuLV-related retroviruses which have been isolated to date, as well as several endogenous examples, fall into the first group, whereas the second group is represented solely by endogenous representatives, including human endogenous retrovirus type E (HERV.E). The two groups are widespread within mammals, with both often present within one animal species. Despite this, there is no evidence to date that recombination between members of the different groups has occurred. Genetic distances and several other properties of the HERV.E genome suggest that if exogenous members of this subgroup exist, they are likely to have biological properties different from those of the other exogenous viruses of this genus. Several of these viruses are known to have been integrated within their hosts' genomes for a long period of time, and a most recent divergence date for the MuLV and HERV.E subgroups can thus be proposed. This date, approximately 30 million years ago, is the most recent date possible, and it is probable that the actual period of time since their divergence is significantly longer.     

How Poxviruses Oppose Apoptosis

Poxviruses express a variety of proteins that are able to modulate the innate cellular apoptotic response triggered by virus infection. Poxviruses are the only DNA viruses to replicate exclusively in the cytoplasm of infected cells, and to date, members of this family have been shown to encode a wide variety of proteins that block or delay apoptosis, including caspase inhibitors, other serpins, death domain effectors, bcl-2/CED-9 homologs, modulators of the FAS/TNF pathway, and inhibitors of PKR. It is predicted that this list of poxvirus apoptosis modulators will continue to grow in the coming years and should provide an increasingly rich and diverse family of apoptosis regulators.     

Method for Extracting Viral Hemagglutination-Inhibiting Antibodies from the Nonspecific Inhibitors of Serum

Various methods are used to remove nonspecific inhibitors from sera before titering viral hemagglutination-inhibiting antibodies. These methods have several undesirable features; some are tedious and time-consuming, some remove antibody along with nonspecific inhibitors, and different techniques are usually required to remove the nonspecific inhibitors for different viruses. This communication describes a single method that uses diethylaminoethyl-Sephadex to extract the immunoglobulin G antibodies for several viruses from nonspecific inhibitors. The procedure is fast, simple to perform, and removed the nonspecific inhibitors for influenza, Western equine encephalitis, dengue-2, and rubella viruses.