Identification, design and bio-evaluation of novel Hsp90 inhibitors by ligand-based virtual screening

QSAR and molecular docking studies on designing potent inhibitors of SARS-CoVs main protease

Background: Severe acute respiratory syndrome coronavirus (SARS-CoVs) have emerged as a global health threat, which had caused a high rate of mortality. There is an urgent need to find effective drugs against these viruses. Objective: This study aims to predict the activity of unsymmetrical aromatic disulfides by constructing a QSAR model, and to design new compounds according to the structural and physicochemical attributes responsible for higher activity towards SARS-CoVs main protease. Methods: All molecules were constructed in ChemOffice software and molecular descriptors were calculated by CODESSA software. A regression-based linear heuristic method was established by changing descriptors datasets and calculating predicted IC₅₀ values of compounds. Then, some new compounds were designed according to molecular descriptors from the heuristic method model. The compounds with predicted values smaller than a set point were constantly screened out. Finally, the properties analysis and molecular docking were conducted to further understand the structure-activity relationships of these finalized compounds. Results: The heuristic method explored the various descriptors responsible for bioactivity and gained the best linear model with R² 0.87. The success of the model fully passed the testing set validation, proving that the model has both high statistical significance and excellent predictive ability. A total of 5 compounds with ideal predicted IC₅₀ were found from the 96 newly designed derivatives and their properties analyze was carried out. Molecular docking experiments were conducted for the optimal compound 31a, which has the best compound activity with good target protein binding capability. Conclusion: The heuristic method was quite reliable for predicting IC₅₀ values of unsymmetrical aromatic disulfides. The present research provides meaningful guidance for further exploration of the highly active inhibitors for SARS-CoVs.

Abdallah M, M. Mukhtar R, Moutasim F, Rafie Ahmed A, Edris A, Ibraheem W, Makki AA, M. Elshamly E, Elhag R, Osman W, A. Mothana R, Alzain AA. Identification of Novel Natural Dual HDAC and Hsp90 Inhibitors for Metastatic TNBC Using e-Pharmacophore Modeling, Molecular Docking, and Molecular Dynamics Studies

Breast cancer (BC) is one of the main types of cancer that endangers women's lives. The characteristics of triple-negative breast cancer (TNBC) include a high rate of recurrence and the capacity for metastasis; therefore, new therapies are urgently needed to combat TNBC. Dual targeting HDAC6 and Hsp90 has shown good synergistic effects in treating metastatic TNBC. The goal of this study was to find potential HDAC6 and Hsp90 dual inhibitors. Therefore, several in silico approaches have been used. An e-pharmacophore model generation based on the HDAC6-ligand complex and subsequently a pharmacophore-based virtual screening on 270,450 natural compounds from the ZINC were performed, which resulted in 12,663 compounds that corresponded to the obtained pharmacophoric hypothesis. These compounds were docked into HDAC6 and Hsp90. This resulted in the identification of three compounds with good docking scores and favorable free binding energy against the two targets. The top three compounds, namely ZINC000096116556, ZINC000020761262, and ZINC000217668954, were further subjected to ADME prediction and molecular dynamic simulations, which showed promising results in terms of pharmacokinetic properties and stability. As a result, these three compounds can be considered potential HDAC6 and Hsp90 dual inhibitors and are recommended for experimental evaluation.

Quantitative structure activity relationship and molecular simulations for the exploration of natural potent VEGFR-2 inhibitors: an in silico anti-angiogenic study

VEGFR-2 has recently become an eye-catching molecular target for the novel therapeutic designs against cancer for its well known role in persuading angiogenesis in tumor cells. The current study set sights on the exploration of novel potent natural compound targeting VEGFR-2 via computational ligand-based modeling and database screening followed by binding pattern analysis, reactivity site prediction and MD simulation studies. The known 53 VEGFR-2 inhibitors (with IC50 ranging from 0.7 nM to 9700 nM) were headed for development of Ligand based pharmacophore model using 3 D QSAR pharmacophore generation module of DS Client. Training set inhibitors (23 compounds) were exploited to create pharmacophore model based on their chemical features. The model was validated through 30 test set inhibitors and exploited further for screening of 62,082 natural compounds from InterBioscreen natural compound database. Screened compounds further went through Drug-Likeliness study, ADMET prediction, Binding pattern analysis, In silico prediction of reactivity sites, Biological activity spectra prediction, pan assay interference compound identification and MD simulation analysis. Out of 5 screened compounds, Compound A and Compound B exhibited highest binding energy judged against the standard drug "Sorafenib". On further conducting reactivity site prediction, BAS prediction, and pan assay interference compound identification, Compound B exhibited better result which was carried forward for MD simulation study for 50 ns. MD simulation results suggested that Compound B exhibited more stable binding to the active site of VEGFR-2 without causing any conformational changes in protein-ligand complex. Thereby, the investigation proposes Compound B to hold potent antiangiogenic potential targeting VEGFR-2. [Formula: see text] Communicated by Ramaswamy H. Sarma.

Identification of inhibitors of the E. coli chaperone SurA using in silico and in vitro techniques

SurA is a gram-negative, periplasmic chaperone protein involved in the proper folding of outer membrane porins (OMPs), which protect bacteria against toxins in the extracellular environment by selectively regulating the passage of nutrients into the cell. Previous studies demonstrated that deletion of SurA renders bacteria more sensitive to toxins that compromise the integrity of the outer membrane. Inhibitors of SurA will perturb the folding of OMPs, leading to disruption of the outer membrane barrier and making the cell more vulnerable to toxic insults. The discovery of novel SurA inhibitors is therefore of great importance for developing alternative strategies to overcome antibiotic resistance. Our laboratory has screened over 10,000,000 compoundsin silicoby computationally docking these compounds onto the crystal structure of SurA. Through this screen and a screen of fragment compounds (molecular weight less than 250 g/mol), we found twelve commercially readily available candidate compounds that bind to the putative client binding site of SurA. We confirmed binding to SurA by developing and employing a competitive fluorescence anisotropy-based binding assay. Our results show that one of these compounds, Fmoc-β-(2-quinolyl)-d-alanine, binds the client binding site with high micromolar affinity. Using this compound as a lead, we also discovered that Fmoc-l-tryptophan and Fmoc-l-phenylalanine, but not Fmoc-l-tyrosine, bind SurA with similar micromolar affinity. To our knowledge, this is the first report of a competitive fluorescence anisotropy assay developed for the identification of inhibitors of the chaperone SurA, and the identification of three small molecules that bind SurA at its client binding site.

Reverse the Resistance to PARP Inhibitors

One of the DNA repair machineries is activated by Poly (ADP-ribose) Polymerase (PARP) enzyme. Particularly, this enzyme is involved in repair of damages to single-strand DNA, thus decreasing the chances of generating double-strand breaks in the genome. Therefore, the concept to block PARP enzymes by PARP inhibitor (PARPi) was appreciated in cancer treatment. PARPi has been designed and tested for many years and became a potential supplement for the conventional chemotherapy. However, increasing evidence indicates the appearance of the resistance to this treatment. Specifically, cancer cells may acquire new mutations or events that overcome the positive effect of these drugs. This paper describes several molecular mechanisms of PARPi resistance which were reported most recently, and summarizes some strategies to reverse this type of drug resistance.

Interaction with specific HSP90 residues as a scoring function: validation in the D3R Grand Challenge 2015

Here is reported the development of a novel scoring function that performs remarkably well at identifying the native binding pose of a subset of HSP90 inhibitors containing aminopyrimidine or resorcinol based scaffolds. This scoring function is called PocketScore, and consists of the interaction energy between a ligand and three residues in the binding pocket: Asp93, Thr184 and a water molecule. We integrated PocketScore into a molecular docking workflow, and used it to participate in the Drug Design Data Resource (D3R) Grand Challenge 2015 (GC2015). PocketScore was able to rank 180 molecules of the GC2015 according to their binding affinity with satisfactory performance. These results indicate that the specific residues considered by PocketScore are determinant to properly model the interaction between HSP90 and its subset of inhibitors containing aminopyrimidine or resorcinol based scaffolds. Moreover, the development of PocketScore aimed at improving docking power while neglecting the prediction of binding affinities, suggesting that accurate identification of native binding poses is a determinant factor for the performance of virtual screens.

Synthesis and evaluation of 4-(2-hydroxypropyl)piperazin-1-yl) derivatives as Hsp90 inhibitors

We previously reported 4-(3-((6-bromonaphthalen-2-yl)oxy)-2-hydroxypropyl)-N,N-dimethylpiperazine-1-sulfonamide (1) as a novel heat shock protein 90 inhibitor with moderate activity. In our ongoing efforts for the discovery of Hsp90 modulators we undertake structural investigations on 1. Series of the titled compound were designed, synthesized and evaluated. We have found that compounds with a hydroxyl group at C-4 of the aryl ring on the piperazine moiety possess Hsp90 inhibition properties. Compound 6f with improved activity could be further developed and optimized as Hsp90 inhibitor.

CPUY201112, a novel synthetic small-molecule compound and inhibitor of heat shock protein Hsp90, induces p53-mediated apoptosis in MCF-7 cells

Heat-shock protein 90 (Hsp90) is highly expressed in many tumor cells and is associated with the maintenance of malignant phenotypes. Targeting Hsp90 has had therapeutic success in both solid and hematological malignancies, which has inspired more studies to identify new Hsp90 inhibitors with improved clinical efficacy. Using a fragment-based approach and subsequent structural optimization guided by medicinal chemistry principles, we identified the novel compound CPUY201112 as a potent Hsp90 inhibitor. It binds to the ATP-binding pocket of Hsp90 with a kinetic dissociation (K_d) constant of 27 ± 2.3 nM. It also exhibits potent in vitro antiproliferative effects in a range of solid tumor cells. In MCF-7 cells with high Hsp90 expression, CPUY201112 induces the degradation of Hsp90 client proteins including HER-2, Akt, and c-RAF. We prove that treating MCF-7 cells with CPUY201112 results in cell cycle arrest and apoptosis through the wild-type (wt) p53 pathway. CPUY201112 also synergizes with Nutlin-3a to induce cancer cell apoptosis. CPUY201112 significantly inhibited the growth of MCF-7 xenografts in nude mice without apparent body weight loss. These results demonstrate that CPUY201112 is a novel Hsp90 inhibitor with potential use in treating wild-type p53 related cancers.

Post-HTS case report and structural alert: Promiscuous 4-aroyl-1,5-disubstituted-3-hydroxy-2H-pyrrol-2-one actives verified by ALARM NMR

Despite its wide use, not every high-throughput screen (HTS) yields chemical matter suitable for drug development campaigns, and seldom are 'go/no-go' decisions in drug discovery described in detail. This case report describes the follow-up of a 4-aroyl-1,5-disubstituted-3-hydroxy-2H-pyrrol-2-one active from a cell-free HTS to identify small-molecule inhibitors of Rtt109-catalyzed histone acetylation. While this compound and structural analogs inhibited Rtt109-catalyzed histone acetylation in vitro, further work on this series was halted after several risk mitigation strategies were performed. Compounds with this chemotype had a poor structure-activity relationship, exhibited poor selectivity among other histone acetyltransferases, and tested positive in a β-lactamase counter-screen for chemical aggregates. Furthermore, ALARM NMR demonstrated compounds with this chemotype grossly perturbed the conformation of the La protein. In retrospect, this chemotype was flagged as a 'frequent hitter' in an analysis of a large corporate screening deck, yet similar compounds have been published as screening actives or chemical probes versus unrelated biological targets. This report-including the decision-making process behind the 'no-go' decision-should be informative for groups engaged in post-HTS triage and highlight the importance of considering physicochemical properties in early drug discovery.

Heat-shock protein 90 (Hsp90) as anticancer target for drug discovery: an ample computational perspective

There are over 100 different types of cancer, and each is classified based on the type of cell that is initially affected. If left untreated, cancer can result in serious health problems and eventually death. Recently, the paradigm of cancer chemotherapy has evolved to use a combination approach, which involves the use of multiple drugs each of which targets an individual protein. Inhibition of heat-shock protein 90 (Hsp90) is one of the novel key cancer targets. Because of its ability to target several signaling pathways, Hsp90 inhibition emerged as a useful strategy to treat a wide variety of cancers. Molecular modeling approaches and methodologies have become 'close counterparts' to experiments in drug design and discovery workflows. A wide range of molecular modeling approaches have been developed, each of which has different objectives and outcomes. In this review, we provide an up-to-date systematic overview on the different computational models implemented toward the design of Hsp90 inhibitors as anticancer agents. Although this is the main emphasis of this review, different topics such as background and current statistics of cancer, different anticancer targets including Hsp90, and the structure and function of Hsp90 from an experimental perspective, for example, X-ray and NMR, are also addressed in this report. To the best of our knowledge, this review is the first account, which comprehensively outlines various molecular modeling efforts directed toward identification of anticancer drugs targeting Hsp90. We believe that the information, methods, and perspectives highlighted in this report would assist researchers in the discovery of potential anticancer agents.

Discovery and Bioevaluation of Novel Pyrazolopyrimidine Analogs as Competitive Hsp90 Inhibitors Through Shape-Based Similarity Screening

Hsp90 as a promising therapeutic target for the treatment of cancer has received great attention. Many Hsp90 inhibitors such as BIIB021 and CUDC-305 have been in clinical. In this paper shape-based similarity screening through ROCS overlays on the basis of CUDC-305, BIIB021, PU-H71 and PU-3 were performed to discover HSP90 inhibitors. A set of 19 novel pyrazolopyrimidine analogues was identified and evaluated on enzyme level and cell-based level as Hsp90 inhibitors. The compound HDI4-04 with IC50 0.35 µM in the Hsp90 ATP hydrolysis assay exhibited potent cytotoxicity against five human cancer cell lines. Western blot analysis and Hsp70 luciferase reporter assay further confirmed that HDI4-04 targeted the Hsp90 protein folding machinery. And according to the biological assay, the SAR was discussed and summarized, which will guide us for further optimization of these compounds.

Hsp90 inhibitors, part 1: definition of 3-D QSAutogrid/R models as a tool for virtual screening

The multichaperone heat shock protein (Hsp) 90 complex mediates the maturation and stability of a variety of oncogenic signaling proteins. For this reason, Hsp90 has emerged as a promising target for anticancer drug development. Herein, we describe a complete computational procedure for building several 3-D QSAR models used as a ligand-based (LB) component of a comprehensive ligand-based (LB) and structure-based (SB) virtual screening (VS) protocol to identify novel molecular scaffolds of Hsp90 inhibitors. By the application of the 3-D QSAutogrid/R method, eight SB PLS 3-D QSAR models were generated, leading to a final multiprobe (MP) 3-D QSAR pharmacophoric model capable of recognizing the most significant chemical features for Hsp90 inhibition. Both the monoprobe and multiprobe models were optimized, cross-validated, and tested against an external test set. The obtained statistical results confirmed the models as robust and predictive to be used in a subsequent VS.