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1.
Chem Biol Drug Des ; 103(1): e14401, 2024 01.
Article in English | MEDLINE | ID: mdl-37985015

ABSTRACT

The human immunodeficiency virus type 1 (HIV-1) Gag protein is responsible for facilitating HIV-1 virion assembly and budding. Our study demonstrates that cardiolipin (CL), a component found in the inner mitochondrial membrane, exhibits the highest binding affinity to the N-terminal MA domain of the HIV-1 Gag protein within the lipid group of host cells. To assess this binding interaction, we synthesized short acyl chain derivatives of CL and employed surface plasmon resonance (SPR) analysis to determine the dissociation constants (Kd) for CL and the MA domain. Simultaneously, we examined the Kd of D-myo-phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2 ) derivatives, known to play a crucial role in virion formation. Among all the derivatives, Tetra-C7 -CL exhibited the lowest Kd value (Kd = 30.8 ± 6.9 µM) for MA binding on the CL analog-immobilized sensorchip, indicating a higher affinity. Similarly, the Kd value of Di-C7 -PIP2 (Kd = 36.6 ± 4.7 µM) was the lowest on the PI(4,5)P2 analog-immobilized sensorchip. Thus, Tetra-C7 -CL binds to the MA domain using a distinct binding mode while displaying a comparable binding affinity to Di-C7 -PIP2. This discovery holds significant implications for comprehending the virological importance of CL-MA domain binding, such as its subcellular distribution, including mitochondrial translocation, and involvement in viral particle formation in concert with PI(4,5)P2 . Furthermore, this study has the potential to contribute to the development of drugs in the future.


Subject(s)
HIV-1 , Humans , Cell Membrane/metabolism , HIV-1/metabolism , Cardiolipins/analysis , Cardiolipins/metabolism , Protein Binding , Gene Products, gag/analysis , Gene Products, gag/metabolism
2.
Pharmaceuticals (Basel) ; 16(11)2023 Nov 14.
Article in English | MEDLINE | ID: mdl-38004473

ABSTRACT

Tumor necrosis factor receptor-associated factors (TRAFs) are a protein family with a wide variety of roles and binding partners. Among them, TRAF6, a ubiquitin ligase, possesses unique receptor binding specificity and shows diverse functions in immune system regulation, cellular signaling, central nervous system, and tumor formation. TRAF6 consists of an N-terminal Really Interesting New Gene (RING) domain, multiple zinc fingers, and a C-terminal TRAF domain. TRAF6 is an important therapeutic target for various disorders and structural studies of this protein are crucial for the development of next-generation therapeutics. Here, we presented a TRAF6 N-terminal structure determined at the Turkish light source "Turkish DeLight" to be 3.2 Å resolution at cryogenic temperature (PDB ID: 8HZ2). This structure offers insight into the domain organization and zinc-binding, which are critical for protein function. Since the RING domain and the zinc fingers are key targets for TRAF6 therapeutics, structural insights are crucial for future research. Separately, we rationally designed numerous new compounds and performed molecular docking studies using this template (PDB ID:8HZ2). According to the results, 10 new compounds formed key interactions with essential residues and zinc ion in the N-terminal region of TRAF6. Molecular dynamic (MD) simulations were performed for 300 ns to evaluate the stability of three docked complexes (compounds 256, 322, and 489). Compounds 256 and 489 was found to possess favorable bindings with TRAF6. These new compounds also showed moderate to good pharmacokinetic profiles, making them potential future drug candidates as TRAF6 inhibitors.

3.
Bioorg Med Chem ; 91: 117408, 2023 08 15.
Article in English | MEDLINE | ID: mdl-37453188

ABSTRACT

Infection with the retrovirus human T-cell leukemia virus type 1 (HTLV-1) sometimes causes diseases that are difficult to cure. To find anti-HTLV-1 natural compounds, we opted to screen using the HTLV-1-infected T-cell line, MT-2. Based on our results, an extract of the pulp/seeds of Akebia quinata Decaisne fruit killed MT-2 cells but did not affect the Jurkat cell line that was not infected with virus. To determine the active ingredients, seven saponins with one-six sugar moieties were isolated from A. quinata seeds, and their activities against the two cell lines were examined. Both cell lines were killed in a similar manner by Akebia saponins A and B. Further, Akebia saponins D, E, PK and G did not exhibit cytotoxicity. Akebia saponin C had a similar activity to the extract found in the screening. This compound was found to enhance Gag aggregation, induce the abnormal cleavage of Gag, suppress virion release, and preferentially kill HTLV-1 infected cells; however, their relationship remains elusive. Our findings may lead to the development of new therapies for infectious diseases based on the removal of whole-virus-infected cells.


Subject(s)
Human T-lymphotropic virus 1 , Saponins , Humans , Cell Line , Saponins/pharmacology , Jurkat Cells , Plant Extracts
4.
Bioorg Med Chem ; 86: 117294, 2023 05 15.
Article in English | MEDLINE | ID: mdl-37141680

ABSTRACT

Drug repurposing is a distinguished approach for drug development that saves a great deal of time and money. Based on our previous successful repurposing of a compound BMMP from anti-HIV-1 therapy to anti-cancer metastatic activity, we adopted the same techniques for repurposing benzimidazole derivatives considering MM-1 as a lead compound. An extensive structure-activity relationship (SAR) study afforded three promising compounds, MM-1d, MM-1h, and MM-1j, which inhibited cell migration in a similar fashion to BMMP. These compounds suppressed CD44 mRNA expression, whereas only MM-1h further suppressed mRNA expression of the epithelial-mesenchymal transition (EMT) marker zeb 1. Using benzimidazole instead of methyl pyrimidine as in BMMP resulted in better affinity for heterogeneous nuclear ribonucleoprotein (hnRNP) M protein and higher anti-cell migration activity. In conclusion, our study identified new agents that surpass the affinity of BMMP for hnRNP M and have anti-EMT activity, which makes them worthy of future attention and optimization.


Subject(s)
Drug Repositioning , Heterogeneous-Nuclear Ribonucleoprotein Group M , Cell Line, Tumor , Cell Migration Inhibition , RNA, Messenger/genetics
5.
Virus Evol ; 8(2): veac060, 2022.
Article in English | MEDLINE | ID: mdl-35903148

ABSTRACT

Characterizing the detailed spatial and temporal dynamics of plant pathogens can provide valuable information for crop protection strategies. However, the epidemiological characteristics and evolutionary trajectories of pathogens can differ markedly from one country to another. The most widespread and important virus of brassica vegetables, turnip mosaic virus (TuMV), causes serious plant diseases in Japan. We collected 317 isolates of TuMV from Raphanus and Brassica plants throughout Japan over nearly five decades. Genomic sequences from these isolates were combined with published sequences. We identified a total of eighty-eight independent recombination events in Japanese TuMV genomes and found eighty-two recombination-type patterns in Japan. We assessed the evolution of TuMV through space and time using whole and partial genome sequences of both nonrecombinants and recombinants. Our results suggest that TuMV was introduced into Japan after the country emerged from its isolationist policy (1639-1854) in the Edo period and then dispersed to other parts of Japan in the 20th century. The results of our analyses reveal the complex structure of the TuMV population in Japan and emphasize the importance of identifying recombination events in the genome. Our study also provides an example of surveying the epidemiology of a virus that is highly recombinogenic.

6.
Chem Pharm Bull (Tokyo) ; 70(7): 477-482, 2022.
Article in English | MEDLINE | ID: mdl-35786566

ABSTRACT

1,2-Naphthoquinone (2-NQ) is a nucleophile acceptor that non-selectively makes covalent bonds with cysteine residues in various cellular proteins, and is also found in diesel exhaust, an air pollutant. This molecule has rarely been considered as a pharmacophore of bioactive compounds, in contrast to 1,4-naphthoquinone. We herein designed and synthesized a compound named N-(7,8-dioxo-7,8-dihydronaphthalen-1-yl)-2-methoxybenzamide (MBNQ), in which 2-NQ was hybridized with the nuclear factor-κB (NF-κB) inhibitor dehydroxymethylepoxyquinomicin (DHMEQ) as a nucleophile acceptor. Although 50 µM MBNQ did not inhibit NF-κB signaling, 10 µM MBNQ induced cell death in the lung cancer cell line A549, which was insensitive to 2-NQ (10 µM). In contrast, MBNQ was less toxic in normal lung cells than 2-NQ. A mechanistic study showed that MBNQ mainly induced apoptosis, presumably via the activation of p38 mitogen-activated protein kinase (MAPK). Collectively, the present results demonstrate that the introduction of an appropriate substituent into 2-NQ constitutes a new biologically active entity, which will lead to the development of 2-NQ-based drugs.


Subject(s)
Lung Neoplasms , Naphthoquinones , Apoptosis , Humans , Lung Neoplasms/drug therapy , NF-kappa B/metabolism , Naphthoquinones/pharmacology
7.
Chem Biol Drug Des ; 99(4): 573-584, 2022 04.
Article in English | MEDLINE | ID: mdl-34882966

ABSTRACT

Various chimeric receptors have been developed and used for biological experiments. In the present study, we constructed three types of chimeric receptor activator of nuclear factor-kappa B (RANK) with the glutathione S-transferase (GST) protein in the extracellular domain, and stimulated them using newly synthesized chemical trimerizers with three glutathiones. Although this stimulation did not activate these proteins, we unexpectedly found that the chimera named RANK-GST-SC, in which GST replaced a major part of the RANK extracellular domain, activated nuclear factor-kappa B (NF-κB) signaling approximately sixfold more strongly than wild-type RANK without the ligand. The dimerization of extracellular GST is considered to function as a switch outside the cell, and signal transduction then occurs. GST has been widely employed as a tag for protein purification; GST-fusion protein can be conveniently captured by glutathione-conjugated beads and easily purified from impurity. The present study is a pioneering example of the novel utility of GST and provides information for the development of new chemical biology systems.


Subject(s)
NF-kappa B , RANK Ligand , Chimera/metabolism , Glutathione Transferase/genetics , Glutathione Transferase/metabolism , Membrane Glycoproteins/chemistry , Membrane Glycoproteins/metabolism , NF-kappa B/metabolism , Osteoclasts/metabolism , Receptor Activator of Nuclear Factor-kappa B/metabolism
8.
Sci Rep ; 11(1): 15819, 2021 08 04.
Article in English | MEDLINE | ID: mdl-34349176

ABSTRACT

Oligomerization of Pr55Gag is a critical step of the late stage of the HIV life cycle. It has been known that the binding of IP6, an abundant endogenous cyclitol molecule at the MA domain, has been linked to the oligomerization of Pr55Gag. However, the exact binding site of IP6 on MA remains unknown and the structural details of this interaction are missing. Here, we present three high-resolution crystal structures of the MA domain in complex with IP6 molecules to reveal its binding mode. Additionally, extensive Differential Scanning Fluorimetry analysis combined with cryo- and ambient-temperature X-ray crystallography and GNM-based transfer entropy calculations identify the key residues that participate in IP6 binding. Our data provide novel insights about the multilayered HIV-1 virion assembly process that involves the interplay of IP6 with PIP2, a phosphoinositide essential for the binding of Pr55Gag to membrane. IP6 and PIP2 have neighboring alternate binding sites within the same highly basic region (residues 18-33). This indicates that IP6 and PIP2 bindings are not mutually exclusive and may play a key role in coordinating virion particles' membrane localization. Based on our three different IP6-MA complex crystal structures, we propose a new model that involves IP6 coordination of the oligomerization of outer MA and inner CA domain's 2D layers during assembly and budding.


Subject(s)
Cell Membrane/metabolism , HIV Infections/metabolism , Phosphoric Monoester Hydrolases/metabolism , Protein Precursors/chemistry , Protein Precursors/metabolism , Binding Sites , Crystallography, X-Ray , HIV Infections/pathology , HIV Infections/virology , HIV-1/physiology , Humans , Models, Molecular , Protein Conformation , Protein Domains , Virus Assembly
9.
Bioorg Chem ; 107: 104627, 2021 02.
Article in English | MEDLINE | ID: mdl-33476868

ABSTRACT

One compound sometimes shows two biological functions, becoming important aspect of recent drug discovery. This study began with an attempt to confirm the previously reported molecular mechanism of the anti-human immunodeficiency virus (HIV) heterocyclic compound BMMP [2-(benzothiazol-2-ylmethylthio)-4-methylpyrimidine], i.e., induction of abnormal uncoating of the viral core at the post-entry step. Our mechanistic study gave results consistent with this mechanism. We further attempted to find out the molecular target of BMMP by a pulldown approach using previously synthesized biotinylated BMMP (Biotin-BMMP) and successfully identified heterogenous nuclear ribonucleoprotein M (hnRNP M) as a BMMP-binding protein. This protein was found not to be accountable for the anti-HIV activity of BMMP. As hnRNP M has been reported to promote cancer metastasis, we tested this mechanism and found that BMMP suppressed migration of the human lung carcinoma cell line A549 stimulated with transforming growth factor-ß (TGF-ß). Mechanistic study showed that BMMP suppressed the expression of CD44 mRNA via the regulation of hnRNP M. Furthermore, six new derivatives of BMMP were synthesized, and the patterns of their activities against HIV-1 and cell migration were not uniform, suggesting that the anti-HIV mechanism and the anti-cell migration mechanism of BMMP are independent. Taken together, the anti-cell migration activity of the anti-HIV heterocyclic compound BMMP was newly discovered by identification of its binding protein hnRNP M using a chemical biology approach.


Subject(s)
Anti-HIV Agents/chemistry , Heterocyclic Compounds/chemistry , Heterogeneous-Nuclear Ribonucleoprotein Group M/metabolism , Anti-HIV Agents/metabolism , Anti-HIV Agents/pharmacology , Cell Line , Cell Movement/drug effects , Down-Regulation/drug effects , Drug Evaluation, Preclinical , Heterocyclic Compounds/metabolism , Heterocyclic Compounds/pharmacology , Heterogeneous-Nuclear Ribonucleoprotein Group M/antagonists & inhibitors , Heterogeneous-Nuclear Ribonucleoprotein Group M/genetics , Humans , Hyaluronan Receptors/genetics , Hyaluronan Receptors/metabolism , Protein Binding , Pyrimidines/chemistry , Pyrimidines/metabolism , Pyrimidines/pharmacology , RNA Interference , RNA, Small Interfering/chemistry , RNA, Small Interfering/metabolism
10.
Bioorg Med Chem Lett ; 30(19): 127458, 2020 10 01.
Article in English | MEDLINE | ID: mdl-32755678

ABSTRACT

Sirtuin proteins are a highly conserved class of nicotinamide adenine dinucleotide (NAD+)-dependent lysine deacylases. The pleiotropic human isoform 2 of Sirtuins (SIRT2) has been engaged in the pathogenesis of cancer in a plethora of reports around the globe. Thus, SIRT2 modulation is deemed as a promising approach for pharmaceutical intervention. Previously, we reported S-Trityl-l-Cysteine (STLC)-ornamented dimethylaminopyridine chemical entity named STC4 with a significant SIRT2 inhibitory capacity; this was separate from the conventional application of STLC scaffold as a kinesin-5 inhibitor. An interactive molecular docking study of SIRT2 and STC4 showed interaction between Asn168 of SIRT2 and the methyl ester of STC4, that appears to hinder STC4 to reach the selective pocket of the protein unlike strong SIRT2 inhibitor SirReal2. To improve its activity, herein, we utilized S-trityl cysteamine pharmacophore lacking the methyl ester. Nine compounds were synthesized and assayed affording three biopertinent SIRT2 inhibitors, and two of them, STCY1 and STCY6 showed higher inhibitory activity than STC4. These compounds have pronounced anti-proliferative activities against different cancer cell lines. A molecular docking study was executed to shed light on the supposed binding mode of the lead compound, STCY1, into the selective pocket of SIRT2 by interaction of the nitrogen of pyridine ring of the compound and Ala135 of the protein. The outcome of the study exposes that the active compounds are effective intermediates to construct more potent biological agents.


Subject(s)
Aminopyridines/pharmacology , Cysteamine/analogs & derivatives , Cysteamine/pharmacology , Histone Deacetylase Inhibitors/pharmacology , Sirtuin 2/antagonists & inhibitors , Trityl Compounds/pharmacology , Aminopyridines/chemical synthesis , Aminopyridines/metabolism , Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/metabolism , Antineoplastic Agents/pharmacology , Cell Line, Tumor , Cell Proliferation/drug effects , Cysteamine/metabolism , Drug Screening Assays, Antitumor , Histone Deacetylase Inhibitors/chemical synthesis , Histone Deacetylase Inhibitors/metabolism , Humans , Molecular Docking Simulation , Molecular Structure , Protein Binding , Sirtuin 2/metabolism , Structure-Activity Relationship , Trityl Compounds/chemical synthesis , Trityl Compounds/metabolism
11.
J Gen Virol ; 101(9): 997-1007, 2020 09.
Article in English | MEDLINE | ID: mdl-32553018

ABSTRACT

The Vpx and Vpr proteins of human immunodeficiency virus type 2 (HIV-2) are important for virus replication. Although these proteins are homologous, Vpx is expressed at much higher levels than Vpr. Previous studies demonstrated that this difference results from the presence of an HHCC zinc-binding site in Vpx that is absent in Vpr. Vpx has another unique region, a poly-proline motif (PPM) of seven consecutive prolines at the C-terminus. Using PPM point mutants of Vpx, this study demonstrated that these seven consecutive prolines are critical for suppressing proteasome degradation of Vpx in the absence of Gag. Both the PPM and the zinc-binding site stabilize Vpx but do so via different mechanisms. PPM and zinc-binding site mutants overexpressed in Escherichia coli aggregated readily, indicating that these motifs normally prevent exposure of the hydrophobic region outside the structure. Furthermore, introduction of the zinc-binding site and the PPM into Vpr increased the level of Vpr expression so that it was as high as that of Vpx. Intriguingly, HIV-2 has evolved to express Vpx at high levels and Vpr at low levels based on the presence and absence of these two motifs with distinct roles.


Subject(s)
Amino Acid Motifs , HIV-2/physiology , Viral Regulatory and Accessory Proteins/chemistry , Viral Regulatory and Accessory Proteins/metabolism , vpr Gene Products, Human Immunodeficiency Virus/chemistry , vpr Gene Products, Human Immunodeficiency Virus/metabolism , Binding Sites , HEK293 Cells , HIV-2/genetics , HeLa Cells , Humans , Mutant Proteins/chemistry , Mutant Proteins/metabolism , Peptides , Point Mutation , Proline/chemistry , Proteasome Endopeptidase Complex/metabolism , Protein Stability , Proteolysis , Viral Regulatory and Accessory Proteins/genetics , Zinc/metabolism , vpr Gene Products, Human Immunodeficiency Virus/genetics
12.
Bioorg Med Chem ; 28(8): 115409, 2020 04 15.
Article in English | MEDLINE | ID: mdl-32169404

ABSTRACT

In 2014, two novel and promising benzimidazole-based APOBEC3G stabilizers MM-1 and MM-2 (MMs) were uncovered with an elusive mechanism of action. Vif-APOBEC3G axis has been recognized as a novel therapeutic target for anti HIV-1 drug development. The unexplored mechanism of MMs hindered their further development into lead compounds. To recognize their underlying mechanism we adopted an exhaustive in silico workflow by which we tested their ability to interrupt Vif complex network formation. The preliminary outcome guided us to a high likelihood of MMs interaction within Elongin C binding site, which in turn, perturbs Vif/Elongin C binding and ultimately undermines Vif action. To validate our estimation, we synthesized only MM-1 as a model to complement our study by in vitro assay for a real-time understanding. An immunoprecipitation experiment confirmed the capacity of MM-1 to interrupt Vif/Elongin C interaction. This is an integral study that lies at the interface between theoretical and experimental approaches showing the potential of molecular modelling to address issues related to drug development.


Subject(s)
APOBEC-3G Deaminase/metabolism , Anti-HIV Agents/pharmacology , Benzimidazoles/pharmacology , HIV-1/metabolism , vif Gene Products, Human Immunodeficiency Virus/metabolism , APOBEC-3G Deaminase/genetics , Anti-HIV Agents/chemical synthesis , Anti-HIV Agents/chemistry , Benzimidazoles/chemistry , Drug Design , Gene Expression Regulation/drug effects , HEK293 Cells , Humans , Molecular Docking Simulation , Molecular Structure , vif Gene Products, Human Immunodeficiency Virus/genetics
13.
Bioorg Med Chem Lett ; 30(7): 127002, 2020 04 01.
Article in English | MEDLINE | ID: mdl-32044184

ABSTRACT

Induction of heat shock protein 70 (HSP70) is known to be effective against various diseases. We are interested in HSP70 induction capability of an antitumor antibiotic bleomycin which produces oxidative stress by iron chelate formation and oxygen activation in a cell. The HSP70 induction activity of bleomycin and its six metal core analogs was examined, and a compound HPH-1Trt of 10 µM was found to induce this protein in a pheochromocytoma cell line and some T cell and monocytic cell lines. Its mechanism is increase of HSP70 mRNA, but higher concentration of this compound showed toxicity. Two new derivatives were then synthesized, and one of them named DHPH-1Trt was shown to have less toxicity and higher HSP70 induction activity. This study would lead to a clue for new HSP70 inducer clinically used in near future.


Subject(s)
HSP70 Heat-Shock Proteins/metabolism , Histidine/analogs & derivatives , Histidine/pharmacology , Pyridines/pharmacology , Animals , Bleomycin/analogs & derivatives , Bleomycin/pharmacology , Bleomycin/toxicity , Cell Line, Tumor , HSP70 Heat-Shock Proteins/genetics , Histidine/toxicity , Macaca , Pyridines/chemical synthesis , Pyridines/toxicity , RNA, Messenger/metabolism , Rats
14.
Molecules ; 24(21)2019 Oct 25.
Article in English | MEDLINE | ID: mdl-31731511

ABSTRACT

Despite the development of a range of anti-cancer agents, cancer diagnoses are still increasing in number, remaining a leading cause of death. Anticancer drug treatment is particularly important for leukemia. We screened Turkish plants and found the unique antileukemic activity of twig components in Turkish Caucasian beech, selectively inducing apoptosis in leukemia cells. This effect is unique among some kinds of beeches, presumably related to oxidative stress. This study would lead to effective use of discarded material, i.e., twig of beech, and a new anti-leukemic drug based on large tree.


Subject(s)
Fagus/chemistry , Leukemia/drug therapy , Plant Extracts/pharmacology , Apoptosis/drug effects , Cell Line, Tumor , Cell Proliferation/drug effects , Humans , Plant Extracts/chemistry , Plant Leaves/chemistry , Trees/chemistry
15.
Bioorg Chem ; 92: 103240, 2019 11.
Article in English | MEDLINE | ID: mdl-31525525

ABSTRACT

Phytic acid (IP6) is an ingredient in cereals and legumes, and limited amounts of this compound are considered to enter the cell and exert anti-cancer effects. These effects have been seen by studying cells treated with around 1-5 mM IP6. However, such a large amount of IP6 chelates metals and changes the pH in cell culture medium. To overcome this problem, we synthesized a prodrug of IP6 (Pro-IP6) and elucidated generation of IP6 from Pro-IP6 in cells. Cellular experiments using Pro-IP6 demonstrated selective anti-cancer effects including apoptosis and inhibition of Akt activation. Furthermore, an in vivo study using mice with adult T-cell leukemia also showed that Pro-IP6 reduced the size of the cancer. Taken together, Pro-IP6 is a useful biological tool and may lead to development of new anti-cancer drugs.


Subject(s)
Antineoplastic Agents/pharmacology , Apoptosis/drug effects , Cell Membrane Permeability/drug effects , Phytic Acid/pharmacology , Prodrugs/pharmacology , Animals , Antineoplastic Agents/chemistry , Antineoplastic Agents/metabolism , Cell Survival/drug effects , Dose-Response Relationship, Drug , HeLa Cells , Humans , Jurkat Cells , K562 Cells , Leukemia, T-Cell/drug therapy , Mice , Molecular Structure , Phytic Acid/chemistry , Phytic Acid/metabolism , Prodrugs/chemistry , Prodrugs/metabolism , Xenograft Model Antitumor Assays
16.
Molecules ; 24(18)2019 Sep 10.
Article in English | MEDLINE | ID: mdl-31510043

ABSTRACT

S-trityl-l-cysteine (STLC) is a well-recognized lead compound known for its anticancer activity owing to its potent inhibitory effect on human mitotic kinesin Eg5. STLC contains two free terminal amino and carboxyl groups that play pivotal roles in binding to the Eg5 pocket. On the other hand, such a zwitterion structure complicates the clinical development of STLC because of the solubility issues. Masking either of these radicals reduces or abolishes STLC activity against Eg5. We recently identified and characterized a new class of nicotinamide adenine dinucleotide-dependent deacetylase isoform 2 of sirtuin protein (SIRT2) inhibitors that can be utilized as cytotoxic agents based on an S-trityl-l-histidine scaffold. Herein, we propose new STLC-derived compounds that possess pronounced SIRT2 inhibition effects. These derivatives contain modified amino and carboxyl groups, which conferred STLC with SIRT2 bioactivity, representing an explicit repurposing approach. Compounds STC4 and STC11 exhibited half maximal inhibitory concentration values of 10.8 ± 1.9 and 9.5 ± 1.2 µM, respectively, against SIRT2. Additionally, introduction of the derivatizations in this study addressed the solubility limitations of free STLC, presumably due to interruption of the zwitterion structure. Therefore, we could obtain drug-like STLC derivatives that work by a new mechanism of action. The new derivatives were designed, synthesized, and their structure was confirmed using different spectroscopic approaches. In vitro and cellular bioassays with various cancer cell lines and in silico molecular docking and solubility calculations of the synthesized compounds demonstrated that they warrant attention for further refinement of their bioactivity.


Subject(s)
Neoplasms/drug therapy , Sirtuin 2/antagonists & inhibitors , Trityl Compounds/pharmacology , Cell Line, Tumor , Computer Simulation , Cysteine/chemistry , Gene Expression Regulation, Neoplastic/drug effects , Humans , Kinesins/chemistry , Kinesins/genetics , Neoplasms/genetics , Neoplasms/pathology , Sirtuin 2/genetics , Solubility , Trityl Compounds/chemistry
17.
Bioorg Med Chem Lett ; 29(16): 2162-2167, 2019 08 15.
Article in English | MEDLINE | ID: mdl-31272791

ABSTRACT

Zinc fingers have rarely been regarded as drug targets. On the contrary, the zinc-binding site of enzymes has often been considered a target of inhibitors. We previously developed a dithiol compound called SN-1 that binds to the zinc finger protein tumor necrosis factor receptor-associated factor 6 (TRAF6) and suppresses downstream nuclear factor-κB (NF-κB) signaling. To determine the minimal structure requirements of TRAF6 inhibitors based on SN-1, NF-κB inhibitory activity and cytotoxicity of its derivatives including new compounds were examined. SN-2, an oxidative type of prodrug of SN-1 with 2-nitrophenylthio groups via disulfide, has the minimum structure for an inhibitor of TRAF6, as seen with cellular experiments. The importance of two side chains with a thiol group was shown with molecular modelling. This study may lead to development of selective TRAF6 inhibitors in the near future.


Subject(s)
TNF Receptor-Associated Factor 6/antagonists & inhibitors , Zinc Fingers/genetics , Humans , Molecular Structure
18.
Int J Mol Sci ; 20(7)2019 Apr 03.
Article in English | MEDLINE | ID: mdl-30987231

ABSTRACT

The Human immunodeficiency virus-1 (HIV-1) matrix (MA) domain is involved in the highly regulated assembly process of the virus particles that occur at the host cell's plasma membrane. High-resolution structures of the MA domain determined using cryo X-ray crystallography have provided initial insights into the possible steps in the viral assembly process. However, these structural studies have relied on large and frozen crystals in order to reduce radiation damage caused by the intense X-rays. Here, we report the first X-ray free-electron laser (XFEL) study of the HIV-1 MA domain's interaction with inositol hexaphosphate (IP6), a phospholipid headgroup mimic. We also describe the purification, characterization and microcrystallization of two MA crystal forms obtained in the presence of IP6. In addition, we describe the capabilities of serial femtosecond X-ray crystallography (SFX) using an XFEL to elucidate the diffraction data of MA-IP6 complex microcrystals in liquid suspension at ambient temperature. Two different microcrystal forms of the MA-IP6 complex both diffracted to beyond 3.5 Å resolution, demonstrating the feasibility of using SFX to study the complexes of MA domain of HIV-1 Gag polyprotein with IP6 at near-physiological temperatures. Further optimization of the experimental and data analysis procedures will lead to better understanding of the MA domain of HIV-1 Gag and IP6 interaction at high resolution and will provide basis for optimization of the lead compounds for efficient inhibition of the Gag protein recruitment to the plasma membrane prior to virion formation.


Subject(s)
HIV-1/chemistry , Temperature , X-Ray Diffraction , gag Gene Products, Human Immunodeficiency Virus/chemistry , Crystallization , Models, Molecular , Protein Domains , Time Factors , Virion/chemistry
19.
Bioorg Med Chem ; 27(9): 1767-1775, 2019 05 01.
Article in English | MEDLINE | ID: mdl-30885568

ABSTRACT

Bleomycin is considered to exert its antitumor activity via DNA cleavage mediated by activated oxygen generated from the iron complex in its chelator moiety. Spin-offs from this moiety, HPH-1Trt and HPH-2Trt, with anti-cancer activities were recently synthesized. In this paper, we developed inhibitors of nicotinamide adenine dinucleotide-dependent deacetylase isoform 2 of Sirtuin protein (SIRT2), based on HPH-1Trt/HPH-2Trt, and aimed to generate new anti-cancer drugs. HPH-1Trt and HPH-2Trt had in vitro anti-SIRT2 inhibitory activity with 50% inhibitory concentration (IC50) values of 5.5 and 8.8 µM, respectively. A structural portion of HPH-1Trt/HPH-2Trt, a tritylhistidine derivative TH-1, had stronger activity (IC50 = 1.7 µM), and thus, fourteen derivatives of TH-1 were synthesized. Among them, TH-3 had the strongest activity (IC50 = 1.3 µM). Selective binding of TH-3 in the pocket of SIRT2 protein was confirmed with a molecular docking study. Furthermore, TH-3 strongly lowered viability of the breast cancer cell line MCF7 with an IC50 of 0.71 µM. A structure-activity relationship study using cell lines suggested that the mechanism of TH-3 to suppress MCF7 cells involves not only SIRT2 inhibition, but also another function. This compound may be a new candidate anti-cancer drug.


Subject(s)
Bleomycin/chemistry , Histidine/chemistry , Histone Deacetylase Inhibitors/chemistry , Sirtuin 2/antagonists & inhibitors , Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacology , Binding Sites , Bleomycin/metabolism , Bleomycin/pharmacology , Catalytic Domain , Cell Survival/drug effects , Histone Deacetylase Inhibitors/metabolism , Histone Deacetylase Inhibitors/pharmacology , Humans , MCF-7 Cells , Molecular Docking Simulation , Sirtuin 2/metabolism , Structure-Activity Relationship
20.
Eur J Med Chem ; 163: 207-214, 2019 Feb 01.
Article in English | MEDLINE | ID: mdl-30522055

ABSTRACT

Ischemia-reperfusion injuries produce reactive oxygen species that promote the peroxide lipid oxidation process resulting in the production of an endogenic lipid peroxide, 4-hydroxy-trans-2-nonenal (4-HNE), a highly cytotoxic aldehyde that induces cell death. We synthesized a novel 4-HNE scavenger - a carnosine-hydrazide derivative, l-carnosine hydrazide (CNN) - and examined its neuroprotective effect in a model of transient ischemia. PC-12 cells were pre-incubated with various doses (0-50 mmol/L) of CNN for 30 min, followed by incubation with 4-HNE (250 µM). An MTT assay was performed 24 h later to examine cell survival. Transient ischemia was induced by bilateral common carotid artery occlusion (BCCO) in the Mongolian gerbil. Animals were assigned to sham-operated (n = 6), placebo-treated (n = 12), CNN pre-treated (20 mg/kg; n = 12), CNN post-treated (100 mg/kg; n = 11), and histidyl hydrazide (a previously known 4-HNE scavenger) post-treated (100 mg/kg; n = 7) groups. Heat shock protein 70 immunoreactivity in the hippocampal CA1 region was evaluated 24 h later, while delayed neuronal death using 4-HNE staining was evaluated 7 days later. Pre-incubation with 30 mmol/L CNN completely inhibited 4-HNE-induced cell toxicity. CNN prevented delayed neuronal death by >60% in the pre-treated group (p < 0.001) and by >40% in the post-treated group (p < 0.01). Histidyl hydrazide post-treatment elicited no protective effect. CNN pre-treatment resulted in high heat shock protein 70 and low 4-HNE immunoreactivity in CA1 pyramidal neurons. Higher 4-HNE immunoreactivity was also found in the placebo-treated animals than in the CNN pre-treated animals. Our novel compound, CNN, elicited highly effective 4-HNE scavenging activity in vitro. Furthermore, CNN administration both pre- and post-BCCO remarkably reduced delayed neuronal death in the hippocampal CA1 region via its induction of heat shock protein 70 and scavenging of 4-HNE.


Subject(s)
CA1 Region, Hippocampal/pathology , Carnosine/pharmacology , Hydrazines/pharmacology , Ischemic Attack, Transient/pathology , Neuroprotective Agents/pharmacology , Aldehydes/metabolism , Animals , CA1 Region, Hippocampal/injuries , Carnosine/chemistry , Cell Death/drug effects , Gerbillinae , HSP70 Heat-Shock Proteins/genetics , Hydrazines/chemistry , Neurons/drug effects , Neuroprotective Agents/chemistry , PC12 Cells , Rats , Reperfusion Injury/metabolism
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