scholarly journals IN SILICO IDENTIFICATION OF APOBEC3B SMALL MOLECULE INHIBITORS FROM DTP-NCI LIBRARIES

Author(s):  
MARYAN MOHAMUD MOHAMED ◽  
NOR ATIQAH JUSRIL ◽  
MOHD ILHAM ADENAN ◽  
N. G. KWOK WEN

Objective: APOBEC3B (A3B) enzyme causes C-to-T or C-to-G somatic alteration in the cancer genome, leading to the evolution of a broad spectrum of human cancers. The present study aims to identify A3B small molecule inhibitors using a top-down approach via pharmacoinformatic virtual screening. Methods: Virtual screening of 2951 drug-alike molecules with diversified structures from the National Cancer Institute Development Therapeutics Program (DTP-NCI) compounds library was performed using GOLD and AutoDock Vina docking programs against the 3D structure of A3B (PDB ID: 5TD5). Results: Amongst the docked compounds, Nordracorubin, NSC641233 and Raloxifene hydrochloride showed the most potent binding affinities towards A3B on both Autodock/Vina and GOLD. Several significant similarities were observed between A3B and the three hits, including hydrogen bonds and pi-pi stacking. The three compounds also exhibited interaction with the centralized zinc cofactor and amino acid residues that directly contribute the deaminase activity of A3B enzyme. Conclusion: We hypothesize that the findings from this study could significantly shorten the quest for novel molecules against the A3B after confirmation with subsequent in vitro and in vivo studies in the near future.

2007 ◽  
Vol 12 (7) ◽  
pp. 983-993 ◽  
Author(s):  
Surya P. Manandhar ◽  
Emily R. Hildebrandt ◽  
Walter K. Schmidt

The Rce1p protease is required for the maturation of the Ras GTPase and certain other isoprenylated proteins and is considered a chemotherapeutic target. To identify new small-molecule inhibitors of Rce1p, the authors screened the National Cancer Institute Diversity Set compound library using in vitro assays to monitor the proteolytic processing of peptides derived from Ras and the yeast a-factor mating pheromone. Of 46 inhibitors initially identified with a Ras-based assay, only 9 were effective in the pheromone-based assay. The IC50 values of these 9 compounds were in the low micromolar range for both yeast (6-35 µM) and human Rce1p (0.4-46 µM). Four compounds were somewhat Rce1p selective in that they partially inhibited the Ste24p protease and did not inhibit Ste14p isoprenylcysteine carboxyl methyltransferase, 2 enzymes also involved in the maturation of isoprenylated proteins. The remaining 5 compounds inhibited all 3 enzymes. The 2 most Rce1p-selective agents were ineffective trypsin inhibitors, further supporting the specificity of these agents for Rce1p. The 5 least specific compounds formed colloidal aggregates, a proposed common feature of promiscuous inhibitors. Interestingly, the most specific Rce1p inhibitor also formed a colloidal aggregate. In vivo studies revealed that treatment of wild-type yeast with 1 compound induced a Ras2p delocalization phenotype that mimics observed effects in rce1 ste24 null yeast. The 9 compounds identified in this study represent new tools for understanding the enzymology of postisoprenylation-modifying enzymes and provide new insight for the future development of Rce1p inhibitors. ( Journal of Biomolecular Screening 2007:983-993)


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 3163-3163
Author(s):  
Rajesh Kumar Gandhirajan ◽  
Iris Gehrke ◽  
Julian Paesler ◽  
Regina Razavi ◽  
Alexandra Filipovich ◽  
...  

Abstract Deregulated WNT signaling has been implicated in variety of tumors. Previous findings suggest critical components of WNT signaling pathway (WNTs, FZD and LEF-1) are overepxressed in B-cell chronic lymphocytic leukemia (CLL) at the m-RNA level. β-catenin (CTNNB1)/LEF-1 transcription activation complex is the key component of WNT signaling which governs the expression of WNT target genes. Critical genes like C-MYC, survivin (SURV), cyclin D1 (CCND1) and LEF-1 which are also overexpressed in CLL are downstream targets of this pathway. In the current study we attempted to inhibit CTNNB1/LEF-1 interaction in CLL cells using the novel small molecule inhibitors CGP049090 and PKF115-584 and observed the survival potential both in vivo and in vitro. Substantial overexpression of LEF-1 and dephospho-CTNNB1, in CLL cells was observed when compared to healthy CD19 positive B cells and PBMCs suggests activation of WNT signaling in CLL. The LC50 calculated from 30 CLL patients was 1.18 μM for CGP049090 and 1.10 μM for PKF115-584 by the ATP based assay. This was confirmed by the DiSC assay LC50 of 0.33 μM (CGP049090) and 0.23 μM (PKF115-584) for primary B-CLL cells (n=3). Both substances showed little effects on normal PBMCs (n=5) as seen from the LC50 values of 90.92 μM and 39.88 μM for CGP049090 and PKF115-584, respectively. Time course experiments indicate activation of caspase 8, 9, 3 & 7, PARP cleavage and paralleled by downregulation of known inhibitors of apoptosis (IAPs) MCL-1, XIAP and BCL-2 leading to apoptosis. Co-immune precipitation of CTNNB1/LEF-1 complex was inhibited in the presence of CGP049090 and PKF115-584 suggesting the specificity of the interaction. Cellular uptake of PKF115-584 and cytoplasmic co-localisation with lef-1 was observed by fluorescence microscopy. In vivo studies reveal that both substances are highly tolerable and effective in eradicating tumor growth in xenografts. The tumor inhibitory rate (IRmax) was found to be 78% and 63.8% for CGP049090 and PKF115-584, respectively. These results indicate that LEF-1 is a promising target for B-CLL therapy as CGP049090 and PKF115-584 effectively induce apoptosis within micromolar concentrations in CLL cells but do not affect healthy cells at these doses. Downregulation of WNT target genes and IAPs hasten the apoptotic mechanism. Moreover, and these inhibitors are highly effective and tolerable in vivo which identifies both compounds as promising drugs for targeted therapy in CLL.


2021 ◽  
Author(s):  
Prosper Obed Chukwuemeka ◽  
Haruna Isiyaku Umar ◽  
Opeyemi Iwaloye ◽  
Oluwaseyi Matthew Oretade ◽  
Christopher Busayo Olowosoke ◽  
...  

Abstract Dysregulation of the p53-MDM2 interactions has been implicated in majority of human tumors presenting a target for finding small molecule inhibitors. In this study, a training set of 17 experimentally tested inhibitors of MDM2 was used to develop series of pharmacophore models among which a four-featured (AHRR_1) model with one hydrogen bond acceptor, one hydrophobic group and two aromatic ring features and characterized by a survival score of 4.176 was considered significant among the top ranked generated hypothesis. Further, the model was validated by an external set of actives and decoy molecules and was found to exhibit encouraging statistical attributes (such as AUC > 0.7, BEDROC > 0.5 and EF > 1.0 etc). The model was used to screen the ZINC compound database, from the database, the top best 1375 hits satisfying the pharmacophore model was were docked to MDM2 protein to identify the likely interactions of the compounds as well as their binding affinity with MDM2. Further, druglikeness and pharmacokinetic properties screening on top-ranked compounds with higher binding affinity than reference inhibitors revealed four compounds (ZINC02639178, ZINC38933175, ZINC77969611, and ZINC06752762) with suitable pharmacological properties including low ligand toxicity. Investigation of the dynamic behaviour of each candidate inhibitors in complex with MDM2 via molecular dynamic simulation suggested ZINC02639178 and ZINC06752762 as the most potential inhibitors. Thus, these compounds may emerged as therapeutic option for cancer treatment after extensive in vitro and in vivo studies.


2001 ◽  
Vol 12 (5) ◽  
pp. 1189-1198 ◽  
Author(s):  
Doron Rapaport ◽  
Rebecca D. Taylor ◽  
Michael Käser ◽  
Thomas Langer ◽  
Walter Neupert ◽  
...  

Tom40 is the major subunit of the translocase of the outer mitochondrial membrane (the TOM complex). To study the assembly pathway of Tom40, we have followed the integration of the protein into the TOM complex in vitro and in vivo using wild-type and altered versions of the Neurospora crassa Tom40 protein. Upon import into isolated mitochondria, Tom40 precursor proteins lacking the first 20 or the first 40 amino acid residues were assembled as the wild-type protein. In contrast, a Tom40 precursor lacking residues 41 to 60, which contains a highly conserved region of the protein, was arrested at an intermediate stage of assembly. We constructed mutant versions of Tom40 affecting this region and transformed the genes into a sheltered heterokaryon containing a tom40 null nucleus. Homokaryotic strains expressing the mutant Tom40 proteins had growth rate defects and were deficient in their ability to form conidia. Analysis of the TOM complex in these strains by blue native gel electrophoresis revealed alterations in electrophoretic mobility and a tendency to lose Tom40 subunits from the complex. Thus, both in vitro and in vivo studies implicate residues 41 to 60 as containing a sequence required for proper assembly/stability of Tom40 into the TOM complex. Finally, we found that TOM complexes in the mitochondrial outer membrane were capable of exchanging subunits in vitro. A model is proposed for the integration of Tom40 subunits into the TOM complex.


Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 306-306
Author(s):  
Meredith W. Miller ◽  
Soni Basra ◽  
Paul C. Billings ◽  
Jamie Gewirtz ◽  
William F. DeGrado ◽  
...  

Abstract Vascular damage due to trauma or disease exposes circulating platelets to collagen in the subendothelial matrix. This is a critical event in the formation of a hemostatic plug or an occluding thrombus because collagen is not only a substrate for platelet adhesion but is also a strong platelet agonist. Platelets possess two physiologic collagen receptors: glycoprotein VI, a member of the immunoglobin superfamily, and the integrin α2β1. To design small molecule inhibitors of the interaction of platelets with collagen, we focused on α2β1 as a target because murine models of α2β1 deficiency display normal bleeding times and only a slight decrease in platelet activation by collagen and because the small number of reported patients with congenital α2β1 deficiency demonstrated only a mild bleeding diathesis. Thus, α2β1 antagonists could be effective anti-thrombotic agents with minimal toxicity, especially when combined with other anti-platelet drugs. We have developed a class of compounds that target the I-like domain of the β1 subunit, an allosteric site that regulates collagen binding to α2β1 by preventing the conversion of α2β1 from an inactive (low affinity) to an active (high affinity) conformation. This class of compounds is based on a proline-substituted 2,3-diaminopropionic acid scaffold. Structure-activity relationship studies of the scaffold have focused on optimization of the proline moiety, the urea functionality, and the sulfonyl group and have resulted in the development of potent inhibitors of α2β1-mediated platelet adhesion to collagen with IC50’s in the high picomolar to low nanomolar range. In particular, optimization of the proline moiety lead to compounds with high potency: transitioning from proline (DB496, IC50 of 29–62 nM) to a thiazolidine (SB68A) improved the IC50 to 2–8 nM; adding a methyl group at the 2 position of the thiazolidine (SB68B) slightly improved the IC50 to 1–12 nM; adding two methyl groups at the 5 position of the thiazolidine (SW4-161) resulted in a lead compound with an IC50 of 0.33–8 nM. As expected, the compounds had no effect on the binding of isolated α2 I-domains to collagen, consistent with their I-like domain mode of activity. Further, they were specific for α2β1-mediated platelet adhesion to collagen because they had no impact on ADP-stimulated platelet aggregation when added at 2 μM, a concentration more than 100-fold greater than the IC50 for inhibition of platelet adhesion to collagen. The compounds were also strong inhibitors of murine platelet adhesion to collagen and when tested in the ferric chloride-initiated murine carotid artery injury model, displayed activity similar to aspirin. Thus, 71% of untreated mice in this thrombosis model developed occlusive thrombi that remained stable for the 30 min duration of the assay, whereas stable thrombi developed in only 32% of mice treated with 1g/kg aspirin orally and in 41% of mice receiving 60 mg/kg CSW4-161intravenously. In summary, we have developed a class of potent inhibitors of the integrin α2β1 that demonstrate both in vitro and in vivo anti-platelet activity. Further development of this class of compounds may result in novel and relatively non-toxic anti-thrombotic agents.


Molecules ◽  
2017 ◽  
Vol 22 (6) ◽  
pp. 1015 ◽  
Author(s):  
Isidro Palos ◽  
Edgar E. Lara-Ramirez ◽  
Julio Cesar Lopez-Cedillo ◽  
Carlos Garcia-Perez ◽  
Muhammad Kashif ◽  
...  

2011 ◽  
Vol 300 (1) ◽  
pp. 30-39 ◽  
Author(s):  
Pramod P. Mehta ◽  
Pei-Pei Kung ◽  
Shinji Yamazaki ◽  
Marlena Walls ◽  
Andrea Shen ◽  
...  

2012 ◽  
Vol 443 (2) ◽  
pp. 549-559 ◽  
Author(s):  
Judith Elkaim ◽  
Michel Castroviejo ◽  
Driss Bennani ◽  
Said Taouji ◽  
Nathalie Allain ◽  
...  

The human protein Pontin, which belongs to the AAA+ (ATPases associated with various cellular activities) family, is overexpressed in several cancers and its silencing in vitro leads to tumour cell growth arrest and apoptosis, making it a good target for cancer therapy. In particular, high levels of expression were found in hepatic tumours for which the therapeutic arsenal is rather limited. The three-dimensional structure of Pontin has been resolved previously, revealing a hexameric assembly with one ADP molecule co-crystallized in each subunit. Using Vina, DrugScore and Xscore, structure-based virtual screening of 2200 commercial molecules was conducted into the ATP-binding site formed by a dimer of Pontin in order to prioritize the best candidates. Complementary to the in silico screening, a versatile and sensitive colorimetric assay was set up to measure the disruption of the ATPase activity of Pontin. This assay allowed the determination of inhibition curves for more than 20 top-scoring compounds, resulting in the identification of four ligands presenting an inhibition constant in the micromolar concentration range. Three of them inhibited tumour cell proliferation. The association of virtual screening and experimental assay thus proved successful for the discovery of the first small-molecule inhibitors of Pontin.


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