scholarly journals In Silico Ligand-Based Methods Targeting Porcupine Receptor Inhibitors with Potential Anticancer Effect

Proceedings ◽  
2018 ◽  
Vol 9 (1) ◽  
pp. 19
Author(s):  
Ana Borota ◽  
Luminita Crisan
Keyword(s):  
Wnt Signaling ◽  
In Silico ◽  
Pharmacophore Model ◽  
Correlation Coefficients ◽  
3D Qsar ◽  
Qsar Model ◽  
Hydrogen Bond Donor ◽  
Screening Process ◽  
Wnt Proteins ◽  
In Silico Study

Porcupine is a protein belonging to the O-acyltransferase family, involved in the catalyzing of palmitoylation of wingless-related integration (WNT) proteins. WNT signaling has significant roles in many physiological functions, e.g., hematopoiesis, homeostasis, neurogenesis, and apoptosis. Anomalous WNT signaling has been observed to be related to tumor generation, and metabolic and neurodegenerative disorders. Therefore, compounds that inhibit this pathway are of great interest for the development of therapeutic approaches. For a better understanding of the common traits of such compounds, we have undertaken an in silico study in order to develop a valid ligand-based pharmacophore model based on a series of porcupine inhibitors. The best pharmacophore hypothesis found after the 3D QSAR validation process is represented by the following features: one hydrogen bond donor (D), three rings (R) and one hydrophobic centroid (H). The 3D-QSAR model obtained using the DRRRH hypothesis shows statistically significant parameters: correlation coefficients for the training set: R2 of 0.90, and a predictive correlation coefficient for the test set, Q2 of 0.86. The assessment of the pharmacophore model was also done and provided very reliable metrics values (Receiver Operating Characteristic—ROC of 1; Robust Initial Enhancement—RIE of 17.97). Thereby, we obtained valuable results which can be further used in the virtual screening process for the discovery of new active compounds with potential anticancer activity.

scholarly journals COMBINATORIAL PHARMACOPHORE MODELING AND ATOM BASED 3D QSAR STUDIES OF BENZOTHIADIAZINES AS HCV-NS5B INHIBITORS

2018 ◽  
Vol 10 (3) ◽  
pp. 43
Author(s):  
Prasanthi Polamreddy ◽  
Vinita Vishwakarma ◽  
Manoj Kumar Mahto
Keyword(s):  
Virtual Screening ◽  
Correlation Coefficient ◽  
Current Model ◽  
Pharmacophore Model ◽  
3D Qsar ◽  
Qsar Model ◽  
Pharmacophore Modeling ◽  
Structural Protein ◽  
Pearson's R ◽  
Pearson’S R

Objective: The objective of the current study was to elucidate the 3D pharmacophoric features of benzothiadiazine derivatives that are crucial for inhibiting Hepatitis C virus (HCV) Non-structural protein 5B (NS5B) and quantifying the features by building an atom based 3D quantitative structure-activity relationship (3D QSAR) model.Methods: Generation of QSAR model was carried out using PHASE 3.3.Results: A five-point pharmacophore model with two hydrogen bond acceptors, one negative ionization potential and two aromatic rings (AANRR) was found to be common among a maximum number of benzothiadiazine based NS5B inhibitors. A statistically significant 3D QSAR model was obtained from AANRR.6 which had correlation-coefficient (R2) value of 0.924, cross-validated correlation-coefficient (Q2) of 0.774, high Fisher ratio of 138 and low root mean square standard error (RMSE=0.29). There is another parameter, Pearson’s R, its value emphasizes correlation between predicted and observed activities of the test set. For the current model, Pearson’s R-value is 0.90, hence underlining the good quality of the model. The present study suggests that nitrogen atom of benzothiadiazine sulfamide ring, oxyacetamide group attached to C7 carbon of benzothiadiazine and sulfonamide oxygens are crucial for NS5B inhibitory activity. Prediction of activities of hit drugs generated in earlier research suggests that Aprepitant (Phase predicted activity: 6.9) could be a potential NS5B inhibitor.Conclusion: This 3D QSAR model developed was statistically good and can be used to predict the activities of newly designed NS5B inhibitors and virtual screening as well. Predict the activities of newly designed NS5B inhibitors and virtual screening as well.

scholarly journals Structure-Based Design and in Silico Screening of Virtual Combinatorial Library of Benzamides Inhibiting 2-trans Enoyl-Acyl Carrier Protein Reductase of Mycobacterium tuberculosis with Favorable Predicted Pharmacokinetic Profiles

2019 ◽  
Vol 20 (19) ◽  
pp. 4730
Author(s):  
Koffi Charles Kouman ◽  
Melalie Keita ◽  
Raymond Kre N’Guessan ◽  
Luc Calvin Owono Owono ◽  
Eugene Megnassan ◽  
...  
Keyword(s):  
Gas Phase ◽  
In Silico ◽  
Combinatorial Library ◽  
Acyl Carrier Protein ◽  
Pharmacophore Model ◽  
Qsar Model ◽  
Active Conformation ◽  
In Silico Screening ◽  
Lipinski’S Rule ◽  
Pharmacokinetic Profiles

Background: During the previous decade a new class of benzamide-based inhibitors of 2-trans enoyl-acyl carrier protein reductase (InhA) of Mycobacterium tuberculosis (Mt) with unusual binding mode have emerged. Here we report in silico design and evaluation of novel benzamide InhA-Mt inhibitors with favorable predicted pharmacokinetic profiles. Methods: By using in situ modifications of the crystal structure of N-benzyl-4-((heteroaryl)methyl) benzamide (BHMB)-InhA complex (PDB entry 4QXM), 3D models of InhA-BHMBx complexes were prepared for a training set of 19 BHMBs with experimentally determined inhibitory potencies (half-maximal inhibitory concentrations IC50exp). In the search for active conformation of the BHMB1-19, linear QSAR model was prepared, which correlated computed gas phase enthalpies of formation (∆∆HMM) of InhA-BHMBx complexes with the IC50exp. Further, taking into account the solvent effect and entropy changes upon ligand, binding resulted in a superior QSAR model correlating computed complexation Gibbs free energies (∆∆Gcom). The successive pharmacophore model (PH4) generated from the active conformations of BHMBs served as a virtual screening tool of novel analogs included in a virtual combinatorial library (VCL) of compounds containing benzamide scaffolds. The VCL filtered by Lipinski’s rule-of-five was screened by the PH4 model to identify new BHMB analogs. Results: Gas phase QSAR model: −log10(IC50exp) = pIC50exp = −0.2465 × ∆∆HMM + 7.95503, R2 = 0.94; superior aqueous phase QSAR model: pIC50exp = −0.2370 × ∆∆Gcom + 7.8783, R2 = 0.97 and PH4 pharmacophore model: p IC 50 exp = 1.0013 × p IC 50 exp − 0.0085, R2 = 0.95. The VCL of more than 114 thousand BHMBs was filtered down to 73,565 analogs Lipinski’s rule. The five-point PH4 screening retained 90 new and potent BHMBs with predicted inhibitory potencies IC50pre up to 65 times lower than that of BHMB1 (IC50exp = 20 nM). Predicted pharmacokinetic profile of the new analogs showed enhanced cell membrane permeability and high human oral absorption compared to current anti-tuberculotics. Conclusions: Combined use of QSAR models that considered binding of the BHMBs to InhA, pharmacophore model, and ADME properties helped to recognize bound active conformation of the benzamide inhibitors, permitted in silico screening of VCL of compounds sharing benzamide scaffold and identification of new analogs with predicted high inhibitory potencies and favorable pharmacokinetic profiles.

In silico study on indole derivatives as anti HIV-1 agents: a combined docking, molecular dynamics and 3D-QSAR study

2013 ◽  
Vol 37 (8) ◽  
pp. 1001-1015 ◽  
Author(s):  
Anand Balupuri ◽  
Changdev G. Gadhe ◽  
Pavithra K. Balasubramanian ◽  
Gugan Kothandan ◽  
Seung Joo Cho
Keyword(s):  
Molecular Dynamics ◽  
In Silico ◽  
3D Qsar ◽  
Indole Derivatives ◽  
Qsar Study ◽  
In Silico Study ◽  
Anti Hiv ◽  
Hiv 1

scholarly journals In silico Design of Novel N-hydrosulfonylbenzamides inhibitors of dengue RNA-dependent RNA polymerase showing favorable predicted pharmacokinetic profiles

2021 ◽  
Vol 5 (2) ◽  
pp. 561-584
Author(s):  
Kouakou Kouakou Jean-Louis ◽  
◽  
Melalie Keita ◽  
Akori Elvice Esmel ◽  
Brice Dali ◽  
...  
Keyword(s):  
Gas Phase ◽  
In Silico ◽  
Pharmacophore Model ◽  
Pharmacokinetic Profile ◽  
Qsar Model ◽  
Active Conformation ◽  
Rna Dependent Rna Polymerase ◽  
In Silico Screening ◽  
Lipinski’S Rule ◽  
Adme Properties

Background: In recent years, there has been a growing interest in Denv NS5 inhibition, with several reported RdRp inhibitors such as sulfonylbenzamides, non-nucleo-side inhibitors without any 3D-QSAR pharmacophore (PH4) available. In this context, we report here, in silico design and virtual evaluation of novel sulfonylbenzamides Denv RdRp inhibitors with favorable predicted pharmacokinetic profile. Methods: By using in situ modifications of the crystal structure of 5-(5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl)-4- methoxy-2-methyl-N-(methylsulfonyl) benzamide (EHB)-RdRp complex (PDB entry 5HMZ), 3D models of RdRp-EHBx complexes were prepared for a training set of 18 EHBs with experimentally determined inhibitory potencies (half-maximal inhibitory concentrations IC50exp). In the search for active conformation of the EHB1-18, linear QSAR model was prepared, which correlated computed gas phase enthalpies of formation ∆∆HMM of RdRp-EHBx complexes with the IC50exp. Further, considering the solvent effect and entropy changes upon ligand binding resulted in a superior QSAR model correlating computed complexation Gibbs free energies (∆∆Gcom). The successive pharmacophore model (PH4) generated from the active conformations of EHBs served as a virtual screening tool of novel analogs included in a virtual combinatorial library (VCL) of compounds with scaffolds restricted to phenyl. The VCL filtered by the Lipinski’s rule-of-five was screened by the PH4 model to identify new EHB analogs. Results: Gas phase QSAR model: -log10(IC50exp) = p IC50exp =-0.1403 x ∆∆HMM _ 7.0879, R2 = 0.73; superior aqueous phase QSAR model: p IC50exp = -0.2036 x ∆∆Gcom + 7.4974, R2 = 0.81 and PH4 pharmacophore model: p IC50exp = 1.0001 x p IC50pre -0.0017, R2 = 0.97. The VCL of more than 30 million EHBs was filtered down to 125,915 analogs Lipinski’s rule. The five-point PH4 screening retained 329 new and potent EHBs with predicted inhibitory potencies p IC50pre up to 30 times lower than that of EHB1 (IC50exp = 23nM). Predicted pharmacokinetic profile of the new analogs showed enhanced cell membrane permeability and high human oral absorption compared to the alone drug to treat dengue virus. Conclusions: Combined use of QSAR models, which considered binding of the EHBs to RdRp, pharmacophore model and ADME properties helped to recognize bound active conformation of the sulfonylbenzamide inhibitors, permitted in silico screening of VCL of compounds sharing sulfonylbenzamide scaffold and identify new analogs with predicted high inhibitory potencies and favorable pharmacokinetic profiles. Keywords: ADME properties prediction, Dengue, 3-(5-ethynylthiophen-2-yl)-N-hydrosulfonylbenzamides, in silico screening, RNA-dependent RNA polymerase.

scholarly journals Revealing ETC-1922159 Affected Unknown 3rd order WNT10B-X-X Combinations, in Silico

2017 ◽  
Author(s):  
shriprakash sinha
Keyword(s):  
Wnt Signaling ◽  
Tumor Cells ◽  
In Silico ◽  
Wnt Signaling Pathway ◽  
In Silico Analysis ◽  
Information Criterion ◽  
Sensitivity Index ◽  
Wnt Proteins ◽  
Wet Lab

WNT10B belongs to the family of WNT proteins that are implicated in a range of phenomena that are affected by the Wnt signaling pathway. Recent studies have shown that WNT10B plays a role in colorectal cancer. WNTs have been found to directly affect the stemness of the tumor cells via regulation of ASCL2. Switching off the ASCL2 literally blocks the stemness process of the tumor cells and vice versa. Furthermore, recent findings suggest BVES to be highly suppressed in malignancies and in vitro deletions of BVES show higher Wnt signaling activity to induce stem- ness. WNT10B was found to be highly expressed in such cases. Often, in biology, we are faced with the problem of exploring relevant unknown biological hypotheses in the form of myriads of combination of factors that might be affecting the pathway under certain conditions. For example, WNT10B-ASCL2 is one such 2nd order combination whose relation needs to be tested under the influence of recently developed porcupine-WNT inhibitor ETC-1922159. The inhibitor is known to suppress PORCN (porcupine) and thus inhibit a range of oncogenes known to be directly or indirectly affected by the Wnts. In a recent unpublished work in bioRxiv, Sinha 1, we had the opportunity to rank these unknown biological hypotheses for down regulated genes at 2nd order level after the drug was administered. The in silico observations showed that the combination of WNT10B-ASCL2 was assigned a relatively lower rank, thus validating the pipeline’s efficacy with the confirmed wet lab experiment that indicate that both WNT10B and ASCL2 were down regulated after treatment in cancer cells. Here, we take one step further by in silico analysis of the 3rd order combinations of WNT10B-X-X (X can be known or unknown factor), from a range of 100 randomly picked down regulated genes after ETC-1922159 treatment. The pipeline uses the density based HSIC (Hilbert Schmidt Information Criterion) sensitivity index with an rbf (ra- dial basis function) kernel, which is known to be highly effective in sensitivity analysis. Various unknown/unexplored/untested 3rd order biological hypotheses emerge some of which are con- firmed in wet lab, while others need to be tested. The potential of such ranking is indispensable in the current era of search in a vast combinatorial forest.

scholarly journals Conformational analysis and molecular design of anthranilic acid derivatives as partial agonists of the Farnesoid X Receptor (FXR) with favorable predicted pharmacokinetic profiles

2021 ◽  
Vol 5 (2) ◽  
pp. 585-600
Author(s):  
Guy Müller Banquet OKRA ◽  
◽  
Dali Brice ◽  
Hermann N'Guessan ◽  
Affiba Florance Kouassi ◽  
...  
Keyword(s):  
Anthranilic Acid ◽  
Molecular Design ◽  
Pharmacophore Model ◽  
3D Qsar ◽  
Qsar Model ◽  
Farnesoid X Receptor ◽  
Virtual Design ◽  
Ligand Complex ◽  
Pharmacokinetic Profiles ◽  
Anthranilic Acid Derivatives

We report here virtual design of new anthranilic acid derivatives (AAD) identified as potent partial Farnesoid X recep-tor (FXR) agonists with favorable predicted pharmacokinetic profiles. By in situ modification of the crystal structure (PDB ID: 3OLF) of FXR complex with a benzimidazole-based partial agonistic ligand, 3D models of 17 FXR:AADx complexes with known observed activity (EC50exp) were prepared to establish a quantitative structure–activity (QSAR) model and linear correla-tion between relative Gibbs free energy (GFE) of receptor-ligand complex formation (Gcom) and EC50exp: pEC50exp = -0,1146 Gcom + 8,175 (#); R2 = 0.98. A 3D QSAR pharmacophore model (PH4) derived from the QSAR directed our effort to design novel AAD analogs. During the design, an initial virtual library of 94501 AAD was focused down to 33134 drug-like compounds and finally, PH4 screened to identify 100 promising compounds. Theoretical EC50 (EC50pre) values of all analogs compounds were predicted by means of equation (#) and their pharmacokinetics (ADME) profiles were computed. More than 12 putative AADs display EC50pre 300 times superior to that of the reported most active training set inhibitor AAD1.

Revealing ETC-1922159 affected unknown 3rd order WNT10B-X-X combinations, in silico

2017 ◽  
Author(s):  
Mengsha Gong ◽  
Kibeom Kim ◽  
Christopher Frick ◽  
Micheal Abrams ◽  
Shriprakash Sinha ◽  
...  
Keyword(s):  
Wnt Signaling ◽  
Tumor Cells ◽  
In Silico ◽  
Wnt Signaling Pathway ◽  
In Silico Analysis ◽  
Information Criterion ◽  
Sensitivity Index ◽  
Wnt Proteins ◽  
Wet Lab

WNT10B belongs to the family of WNT proteins that are implicated in a range of phenomena that are affected by the Wnt signaling pathway. Recent studies have shown that WNT10B plays a role in colorectal cancer. WNTs have been found to directly affect the stemness of the tumor cells via regulation of ASCL2. Switching off the ASCL2 literally blocks the stemness process of the tumor cells and vice versa. Furthermore, recent findings suggest BVES to be highly suppressed in malignancies and in vitro deletions of BVES show higher Wnt signaling activity to induce stemness. WNT10B was found to be highly expressed in such cases. Often, in biology, we are faced with the problem of exploring relevant unknown biological hypotheses in the form of myriads of combination of factors that might be affecting the pathway under certain conditions. For example, WNT10B-ASCL2 is one such 2nd order combination whose relation needs to be tested under the influence of recently developed porcupine-WNT inhibitor ETC-1922159. The inhibitor is known to suppress PORCN (porcupine) and thus inhibit a range of oncogenes known to be directly or indirectly affected by the Wnts. In a recent unpublished work in bioRxiv, we had the opportunity to rank these unknown biological hypotheses for down regulated genes at 2nd order level after the drug was administered. The in silico observations showed that the combination of WNT10B-ASCL2 was assigned a relatively lower rank, thus validating the pipeline's efficacy with the confirmed wet lab experiment that indicate that both WNT10B and ASCL2 were down regulated after treatment in cancer cells. Here, we take one step further by in silico analysis of the 3rd order combinations of WNT10B-X-X (X can be known or unknown factor), from a range of 100 randomly picked down regulated genes after ETC-1922159 treatment. The pipeline uses the density based HSIC (Hilbert Schmidt Information Criterion) sensitivity index with an rbf (radial basis function) kernel, which is known to be highly effective in sensitivity analysis. Various unknown/unexplored/untested 3rd order biological hypotheses emerge some of which are confirmed in wet lab, while others need to be tested. The potential of such ranking is indispensable in the current era of search in a vast combinatorial forest.

scholarly journals Computer-aided Design of Peptidomimetic Inhibitors of falcipain-3: QSAR and Pharmacophore Models

2021 ◽  
Author(s):  
Boris D. Bekono ◽  
Akori Esmel ◽  
Brice Dali ◽  
Fidele Ntie-Kang ◽  
Melalie Keita ◽  
...  
Keyword(s):  
Computer Aided Design ◽  
Molecular Design ◽  
Structural Information ◽  
Three Dimensional ◽  
Pharmacophore Model ◽  
Combinatorial Libraries ◽  
3D Qsar ◽  
3D Models ◽  
Qsar Model ◽  
Computer Aided

In this work antiparasitic peptidomimetics inhibitors (PEP) of falcipain-3 (FP3) of Plasmodium falciparum (Pf) have been proposed using structure-based and computer-aided molecular design. Beginning with the crystal structure of PfFP3-K11017 complex (PDB ID: 3BWK), three-dimensional (3D) models of FP3-PEPx complexes with known activities (IC50exp) were prepared by in situ modification, based on molecular mechanics and implicit solvation to compute Gibbs free energies (GFE) of inhibitor-FP3 complex formation. This resulted in a quantitative structure-activity relationships (QSAR) model based on a linear correlation between computed GFE (ΔΔGcomp) and the experimentally measured IC50exp: (pIC50exp=-(IC50exp/109) =-0.4517×∆∆Gcomp+4.0865 ; R2 = 0.89). Apart from the structure-based relationship, a ligand-based quantitative pharmacophore model (PH4) of novel PEP analogs where substitutions were directed by comparative analysis of the active site interactions was derived using the proposed bound conformations of the PEPx. This provided structural information useful for the design of virtual combinatorial libraries (VL), which was virtually screened based on the 3D-QSAR PH4. The end results were predictory inhibitory activities falling within the low nanomolar concentration range.

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