MyMedR

Fulltext (R)-(+)-α-lipoic acid protected NG108-15 cells against H₂O₂-induced cell death through PI3K-Akt/GSK-3β pathway and suppression of NF-κβ-cytokines

Kamarudin MN, Mohd Raflee NA, Hussein SS, Lo JY, Supriady H, Abdul Kadir H

Drug Des Devel Ther, 2014;8:1765-80.

PMID: 25336920 DOI: 10.2147/DDDT.S67980

Alpha-lipoic acid, a potent antioxidant with multifarious pharmacological benefits has been reported to be neuroprotective in several neuronal models and used to treat neurological disorders such as Alzheimer's disease. Nonetheless, conclusive mechanisms of alpha-lipoic acid for its protective effects particularly in NG108-15 cells have never been investigated. In this study, the intricate neuroprotective molecular mechanisms by (R)-(+)-alpha-lipoic acid (R-LA) against H2O2-induced cell death in an in vitro model of neurodegeneration were elucidated. Pretreatment with R-LA (2 hours) significantly increased NG108-15 cell viability as compared to H2O2-treated cells and mitigated the induction of apoptosis as evidenced by Hoechst 33342/propidium iodide staining. R-LA (12.5-50 μM) aggrandized the reduced glutathione over glutathione disulfide ratio followed by a reduction in the intracellular reactive oxygen species level and an increase in mitochondrial membrane potential following H2O2 exposure. Moreover, pretreatment with R-LA stimulated the activation of PI3K-Akt through mTORC1 and mTORC2 components (mTOR, rictor and raptor) and production of antiinflammatory cytokine, IL-10 which led to the inactivation of glycogen synthase kinase-3β (GSK-3β) and reduction of both Bax/Bcl2 and Bax/Bcl-xL ratios, accompanied by inhibition of the cleaved caspase-3. Additionally, this observation was preceded by the suppression of NF-κβ p65 translocation and production of proinflammatory cytokines (IL-6 and TNF-α). The current findings accentuate new mechanistic insight of R-LA against apoptogenic and brain inflammatory factors in a neuronal model. These results further advocate the therapeutic potential of R-LA for the treatment of neurodegenerative diseases.

Matched MeSH terms: Structure-Activity Relationship

2'-Aryl and 4'-arylidene substituted pyrazolones: As potential α-amylase inhibitors

Yousuf S, Khan KM, Salar U, Chigurupati S, Muhammad MT, Wadood A, et al.

Eur J Med Chem, 2018 Nov 05;159:47-58.

PMID: 30268823 DOI: 10.1016/j.ejmech.2018.09.052

Acarbose and voglibose are well-known α-amylase inhibitors used for the management of type-II diabetes mellitus. Unfortunately, these well-known and clinically used inhibitors are also associated with several adverse effects. Therefore, there is still need to develop the safer therapy. Despite of a broad spectrum of biological significances of pyrazolone, it is infrequently evaluated for α-amylase inhibition. Current study deals with the synthesis and biological screening of aryl and arylidene substituted pyrazolones 1-18 for their potential α-amylase inhibitory activity. Structures of synthetic derivatives 1-18 were identified by different spectroscopic techniques. All compounds 1-18 (IC50 = 1.61 ± 0.16 μM to 2.38 ± 0.09 μM) exhibited significant to moderate inhibitory potential when compared to standard acarbose (IC50 = 1.46 ± 0.26 μM). A number of derivatives including 8-12 (IC50 = 1.68 ± 0.1 μM to 1.97 ± 0.07 μM) and 14-16 (IC50 = 1.61 ± 0.16 μM to 1.93 ± 0.07 μM) were found to be significantly active. Limited SAR suggested that different substitutions on compounds do not have any significant effect on the inhibitory potential. Compounds were found to be mixed-type inhibitors revealed by kinetic studies. However, in silico study was identified a number of key features participating in the interaction with the binding site of α-amylase enzyme.

Matched MeSH terms: Structure-Activity Relationship

2-Aminothiazole-Oxadiazole Bearing N-Arylated Butanamides: Convergent Synthesis, Tyrosinase Inhibition, Kinetics, Structure-Activity Relationship, and Binding Conformations

Raza H, Rehman Sadiq Butt A, Athar Abbasi M, Aziz-Ur-Rehman, Zahra Siddiqui S, Hassan M, et al.

Chem Biodivers, 2023 Feb;20(2):e202201019.

PMID: 36597268 DOI: 10.1002/cbdv.202201019

A multi-step synthesis of novel bi-heterocyclic N-arylated butanamides was consummated through a convergent strategy and the structures of these medicinal scaffolds, 7a-h, were corroborated using spectral techniques. The in vitro analysis of these hybrid molecules revealed their potent tyrosinase inhibition as compared to the standard used. The kinetics mechanism was investigated through Lineweaver-Burk plots which exposed that, 7f, inhibited tyrosinase enzyme non-competitively by forming the enzyme-inhibitor complex. The inhibition constants Ki calculated from Dixon plots for this compound was 0.025 μM. Their binding conformations were ascertained by in silico computational studies whereby these molecules disclosed good binding energy values (kcal/mol). So, it was anticipated from the current research that these bi-heterocyclic butanamides might be probed as imperative therapeutic agents for melanogenesis.

Matched MeSH terms: Structure-Activity Relationship

2-Aryl benzimidazoles: Synthesis, In vitro α-amylase inhibitory activity, and molecular docking study

Adegboye AA, Khan KM, Salar U, Aboaba SA, Kanwal, Chigurupati S, et al.

Eur J Med Chem, 2018 Apr 25;150:248-260.

PMID: 29533872 DOI: 10.1016/j.ejmech.2018.03.011

Despite of many diverse biological activities exhibited by benzimidazole scaffold, it is rarely explored for the α-amylase inhibitory activity. For that purpose, 2-aryl benzimidazole derivatives 1-45 were synthesized and screened for in vitro α-amylase inhibitory activity. Structures of all synthetic compounds were deduced by various spectroscopic techniques. All compounds revealed inhibition potential with IC50 values of 1.48 ± 0.38-2.99 ± 0.14 μM, when compared to the standard acarbose (IC50 = 1.46 ± 0.26 μM). Limited SAR suggested that the variation in the inhibitory activities of the compounds are the result of different substitutions on aryl ring. In order to rationalize the binding interactions of most active compounds with the active site of α-amylase enzyme, in silico study was conducted.

Matched MeSH terms: Structure-Activity Relationship

2-Benzoyl-6-benzylidenecyclohexanone analogs as potent dual inhibitors of acetylcholinesterase and butyrylcholinesterase

Leong SW, Abas F, Lam KW, Shaari K, Lajis NH

Bioorg Med Chem, 2016 08 15;24(16):3742-51.

PMID: 27328658 DOI: 10.1016/j.bmc.2016.06.016

In the present study, a series of 2-benzoyl-6-benzylidenecyclohexanone analogs have been synthesized and evaluated for their anti-cholinesterase activity. Among the forty-one analogs, four compounds (38, 39, 40 and 41) have been identified as lead compounds due to their highest inhibition on both AChE and BChE activities. Compounds 39 and 40 in particular exhibited highest inhibition on both AChE and BChE with IC50 values of 1.6μM and 0.6μM, respectively. Further structure-activity relationship study suggested that presence of a long-chain heterocyclic in one of the rings played a critical role in the dual enzymes' inhibition. The Lineweaver-Burk plots and docking results suggest that both compounds could simultaneously bind to the PAS and CAS regions of the enzyme. ADMET analysis further confirmed the therapeutic potential of both compounds based upon their high BBB-penetrating. Thus, 2-benzoyl-6-benzylidenecyclohexanone containing long-chain heterocyclic amine analogs represent a new class of cholinesterase inhibitor, which deserve further investigation for their development into therapeutic agents for cognitive diseases such as Alzheimer.

Matched MeSH terms: Structure-Activity Relationship

3,4-Dimethoxybenzohydrazide derivatives as antiulcer: Molecular modeling and density functional studies

Taha M, Ismail NH, Zaki HM, Wadood A, Anouar EH, Imran S, et al.

Bioorg Chem, 2017 12;75:235-241.

PMID: 29031169 DOI: 10.1016/j.bioorg.2017.10.004

3,4-Dimethoxybenzohydrazide derivatives (1-25) have been synthesized and evaluated for their urease inhibitory potential. Among the series, compounds 2, 3, 4 and 5 with IC50 values 12.61 ± 0.07, 18.24 ± 0.14, 19.22 ± 0.21, and 8.40 ± 0.05 µM, respectively, showed excellent urease inhibitory potentials when compared with standard thiourea (IC50 value 21.40 ± 0.21 µM). Compounds 1, 6, 8, 18, 19 and 20 also showed good to moderate inhibition, while the remaining compounds were found to be completely inactive. The structures of compounds 6 and 25 were confirmed through X-ray crystallography while the structures of remaining compounds were confirmed through ESI-MS and 1H NMR. Molecular docking studies were performed understand the binding interactions with enzyme active site. The synthesized compounds were evaluated for cytotoxicity and found to be nontoxic.

Matched MeSH terms: Structure-Activity Relationship

3,5-dibenzyloxy-4'-hydroxystilbene induces early caspase-9 activation during apoptosis in human K562 chronic myelogenous leukemia cells

Roslie H, Chan KM, Rajab NF, Velu SS, Kadir SA, Bunyamin I, et al.

J Toxicol Sci, 2012 Feb;37(1):13-21.

PMID: 22293408

A series of 22 stilbene derivatives based on resveratrol were synthesized incorporating acetoxy-, benzyloxy-, carboxy-, chloro-, hydroxy- and methoxy functional groups. We examined the cytotoxicity of these 22 stilbenes in human K562 chronic myelogenous leukemia cells. Only four compounds were cytotoxic namely 4'-hydroxy-3-methoxystilbene (15), 3'-acetoxy-4-chlorostilbene (19), 4'-hydroxy-3,5-dimethoxystilbene or pterostilbene (3) and 3,5-dibenzyloxy-4'-hydroxystilbene (28) with IC(50)s of 78 µM, 38 µM, 67 µM and 19.5 µM respectively. Further apoptosis assessment on the most potent compound, 28, confirmed that the cells underwent apoptosis based on phosphatidylserine externalization and loss of mitochondrial membrane potential. Importantly, we observed a concentration-dependent activation of caspase-9 as early as 2 hr with resultant caspase-3 cleavage in 28-induced apoptosis. Additionally, a structure-activity relationship (SAR) study proposed a possible mechanism of action for compound 28. Taken together, our data suggests that the pro-apoptotic effects of 28 involve the intrinsic mitochondrial pathway characterized by an early activation of caspase-9.

Matched MeSH terms: Structure-Activity Relationship

3-Benzyl(phenethyl)-2-thioxobenzo[g]quinazolines as a new class of potent α-glucosidase inhibitors: synthesis and molecular docking study

Al-Salahi R, Ahmad R, Anouar E, Iwana Nor Azman NI, Marzouk M, Abuelizz HA

Future Med Chem, 2018 08 01;10(16):1889-1905.

PMID: 29882426 DOI: 10.4155/fmc-2018-0141

AIM: Using a simple modification on a previously reported synthetic route, 3-benzyl(phenethyl)-2-thioxobenzo[g]quinazolin-4(3H)-ones (1 and 2) were synthesized with high yields. Further transformation of 1 and 2 produced derivatives 3-26, which were structurally characterized based on NMR and MS data, and their in vitro α-glucosidase inhibitory activity was evaluated using Baker's yeast α-glucosidase enzyme.

RESULTS: Compounds 2, 4, 8, 12 and 20 exhibited the highest activity (IC50 = 69.20, 59.60, 49.40, 50.20 and 83.20 μM, respectively) compared with the standard acarbose (IC50 = 143.54 μM).

CONCLUSION: A new class of potent α-glucosidase inhibitors was identified, and the molecular docking predicted plausible binding interaction of the targets in the binding pocket of α-glucosidase and rationalized the structure-activity relationship (SARs) of the target compounds.

Matched MeSH terms: Structure-Activity Relationship

Fulltext 3D-QSAR modelling dataset of bioflavonoids for predicting the potential modulatory effect on P-glycoprotein activity

Wongrattanakamon P, Lee VS, Nimmanpipug P, Jiranusornkul S

Data Brief, 2016 Dec;9:35-42.

PMID: 27626051 DOI: 10.1016/j.dib.2016.08.004

The data is obtained from exploring the modulatory activities of bioflavonoids on P-glycoprotein function by ligand-based approaches. Multivariate Linear-QSAR models for predicting the induced/inhibitory activities of the flavonoids were created. Molecular descriptors were initially used as independent variables and a dependent variable was expressed as pFAR. The variables were then used in MLR analysis by stepwise regression calculation to build the linear QSAR data. The entire dataset consisted of 23 bioflavonoids was used as a training set. Regarding the obtained MLR QSAR model, R of 0.963, R (2)=0.927, [Formula: see text], SEE=0.197, F=33.849 and q (2)=0.927 were achieved. The true predictabilities of QSAR model were justified by evaluation with the external dataset (Table 4). The pFARs of representative flavonoids were predicted by MLR QSAR modelling. The data showed that internal and external validations may generate the same conclusion.

Matched MeSH terms: Quantitative Structure-Activity Relationship

5-Bromo-2-aryl benzimidazole derivatives as non-cytotoxic potential dual inhibitors of α-glucosidase and urease enzymes

Arshad T, Khan KM, Rasool N, Salar U, Hussain S, Asghar H, et al.

Bioorg Chem, 2017 06;72:21-31.

PMID: 28346872 DOI: 10.1016/j.bioorg.2017.03.007

On the basis of previous report on promising α-glucosidase inhibitory activity of 5-bromo-2-aryl benzimidazole derivatives, these derivatives were further screened for urease inhibitory and cytotoxicity activity in order to get more potent and non-cytotoxic potential dual inhibitor for the patients suffering from diabetes as well as peptic ulcer. In this study, all compounds showed varying degree of potency in the range of (IC50=8.15±0.03-354.67±0.19μM) as compared to standard thiourea (IC50=21.25±0.15μM). It is worth mentioning that derivatives 7 (IC50=12.07±0.05μM), 8 (IC50=10.57±0.12μM), 11 (IC50=13.76±0.02μM), 14 (IC50=15.70±0.12μM) and 22 (IC50=8.15±0.03μM) were found to be more potent inhibitors than standard. All compounds were also evaluated for cytotoxicity towards 3T3 mouse fibroblast cell line and found to be completely non-toxic. Previously benzimidazole 1-25 were also showed α-glucosidase inhibitory potential. In silico studies were performed on the lead molecules i.e.2, 7, 8, 11, 14, and 22, in order to rationalize the binding interaction of compounds with the active site of urease enzyme.

Matched MeSH terms: Structure-Activity Relationship

A "healthy apatite" for bone repair

Best SM, Patel N, Porter AE, Bonfield W

Med J Malaysia, 2004 May;59 Suppl B:129-30.

PMID: 15468852

Bone is unique in its ability to adapt structure to functional requirements, but as is all too obvious in an ever-ageing population it is susceptible to a number of degenerative diseases. Therefore there is an increasing need for materials for bone replacement. Clearly, the ideal material with which to replace bone, would be bone itself, but the major problem now facing us is that there is an insufficient supply of the natural bone to satisfy the clinical requirements. Hence, there is a need for the development of chemically synthesised bone graft substitutes

Matched MeSH terms: Structure-Activity Relationship

A QSAR model for predicting antidiabetic activity of dipeptidyl peptidase-IV inhibitors by enhanced binary gravitational search algorithm

Al-Fakih AM, Algamal ZY, Lee MH, Aziz M, Ali HTM

SAR QSAR Environ Res, 2019 Jun;30(6):403-416.

PMID: 31122062 DOI: 10.1080/1062936X.2019.1607899

Time-varying binary gravitational search algorithm (TVBGSA) is proposed for predicting antidiabetic activity of 134 dipeptidyl peptidase-IV (DPP-IV) inhibitors. To improve the performance of the binary gravitational search algorithm (BGSA) method, we propose a dynamic time-varying transfer function. A new control parameter,
μ
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compared to obtained results by BGSA, indicating the best prediction performance of the proposed TVBGSA model. The results clearly reveal that the proposed TVBGSA method is useful for constructing reliable and robust QSARs for predicting antidiabetic activity of DPP-IV inhibitors prior to designing and experimental synthesizing of new DPP-IV inhibitors.

Matched MeSH terms: Quantitative Structure-Activity Relationship*

Fulltext A Quantum Chemical and Statistical Study of Cytotoxic Activity of Compounds Isolated from Curcuma zedoaria

Hamdi OA, Anouar el H, Shilpi JA, Trabolsy ZB, Zain SB, Zakaria NS, et al.

Int J Mol Sci, 2015 Apr 27;16(5):9450-68.

PMID: 25923077 DOI: 10.3390/ijms16059450

A series of 21 compounds isolated from Curcuma zedoaria was subjected to cytotoxicity test against MCF7; Ca Ski; PC3 and HT-29 cancer cell lines; and a normal HUVEC cell line. To rationalize the structure-activity relationships of the isolated compounds; a set of electronic; steric and hydrophobic descriptors were calculated using density functional theory (DFT) method. Statistical analyses were carried out using simple and multiple linear regressions (SLR; MLR); principal component analysis (PCA); and hierarchical cluster analysis (HCA). SLR analyses showed that the cytotoxicity of the isolated compounds against a given cell line depend on certain descriptors; and the corresponding correlation coefficients (R2) vary from 0%-55%. MLR results revealed that the best models can be achieved with a limited number of specific descriptors applicable for compounds having a similar basic skeleton. Based on PCA; HCA and MLR analyses; active compounds were classified into subgroups; which was in agreement with the cell based cytotoxicity assay.

Matched MeSH terms: Quantitative Structure-Activity Relationship

A facile chemo-, regio- and stereoselective synthesis and cholinesterase inhibitory activity of spirooxindole-pyrrolizine-piperidine hybrids

Kia Y, Osman H, Kumar RS, Murugaiyah V, Basiri A, Perumal S, et al.

Bioorg Med Chem Lett, 2013 May 15;23(10):2979-83.

PMID: 23570788 DOI: 10.1016/j.bmcl.2013.03.027

A series of novel hybrid spiro heterocycles comprising pyrrolizine, spiroxindole and piperidine moieties was synthesized chemo-, regio- and stereoselectively in good yields from 1,3-dipolar cycloaddition reaction of a series of 1-acryloyl-3,5-bisarylmethylidenepiperidin-4-ones with azomethine ylides generated in situ from 5-choloroisatin and l-proline in methanol. These cycloadducts displayed significant cholinesterase inhibitory activity. Among the compounds screened, 8g and 8e, showed maximum inhibitory activity against acetylcholinesterase (AChE) and butyrylcholinestrase (BChE) with IC50 values of 3.33 and 3.13μM, respectively.

Matched MeSH terms: Structure-Activity Relationship

A facile stereoselective synthesis of dispiro-indeno pyrrolidine/pyrrolothiazole-thiochroman hybrids and evaluation of their antimycobacterial, anticancer and AchE inhibitory activities

Bharkavi C, Vivek Kumar S, Ashraf Ali M, Osman H, Muthusubramanian S, Perumal S

Bioorg Med Chem, 2016 11 15;24(22):5873-5883.

PMID: 27687968 DOI: 10.1016/j.bmc.2016.09.044

A facile stereoselective synthesis of novel dispiro indeno pyrrolidine/pyrrolothiazole-thiochroman hybrids has been achieved by 1,3-dipolar cycloaddition of azomethine ylides, generated in situ from ninhydrin and sarcosine/thiaproline, on a series of 3-benzylidenethiochroman-4-ones. The synthesised compounds were screened for their antimycobacterial, anticancer and AchE inhibition activities. Compound 4l (IC50 1.07μM) has been found to exhibit the most potent antimycobacterial activity compared to cycloserine (12 times), pyrimethamine (37 times) and ethambutol (IC50 <1.56μM) and 6l (IC50=2.87μM) is more active than both cycloserine (4 times) and pyrimethamine (12 times). Three compounds, 4a, 6b and 6i, display good anticancer activity against CCRF-CEM cell lines. Compounds 6g and 4g display maximum AchE inhibitory activity with IC50 values of 1.10 and 1.16μmol/L respectively.

Matched MeSH terms: Structure-Activity Relationship

A molecular approach in drug development for Alzheimer's disease

Agatonovic-Kustrin S, Kettle C, Morton DW

Biomed Pharmacother, 2018 Oct;106:553-565.

PMID: 29990843 DOI: 10.1016/j.biopha.2018.06.147

An increase in dementia numbers and global trends in population aging across the world prompts the need for new medications to treat the complex biological dysfunctions, such as neurodegeneration associated with dementia. Alzheimer's disease (AD) is the most common form of dementia. Cholinergic signaling, which is important in cognition, is slowly lost in AD, so the first line therapy is to treat symptoms with acetylcholinesterase inhibitors to increase levels of acetylcholine. Out of five available FDA-approved AD medications, donepezil, galantamine and rivastigmine are cholinesterase inhibitors while memantine, a N-methyl d-aspartate (NMDA) receptor antagonist, blocks the effects of high glutamate levels. The fifth medication consists of a combination of donepezil and memantine. Although these medications can reduce and temporarily slow down the symptoms of AD, they cannot stop the damage to the brain from progressing. For a superior therapeutic effect, multi-target drugs are required. Thus, a Multi-Target-Directed Ligand (MTDL) strategy has received more attention by scientists who are attempting to develop hybrid molecules that simultaneously modulate multiple biological targets. This review highlights recent examples of the MTDL approach and fragment based strategy in the rational design of new potential AD medications.

Matched MeSH terms: Structure-Activity Relationship

A new adaptive L1-norm for optimal descriptor selection of high-dimensional QSAR classification model for anti-hepatitis C virus activity of thiourea derivatives

Algamal ZY, Lee MH

SAR QSAR Environ Res, 2017 Jan;28(1):75-90.

PMID: 28176549 DOI: 10.1080/1062936X.2017.1278618

A high-dimensional quantitative structure-activity relationship (QSAR) classification model typically contains a large number of irrelevant and redundant descriptors. In this paper, a new design of descriptor selection for the QSAR classification model estimation method is proposed by adding a new weight inside L1-norm. The experimental results of classifying the anti-hepatitis C virus activity of thiourea derivatives demonstrate that the proposed descriptor selection method in the QSAR classification model performs effectively and competitively compared with other existing penalized methods in terms of classification performance on both the training and the testing datasets. Moreover, it is noteworthy that the results obtained in terms of stability test and applicability domain provide a robust QSAR classification model. It is evident from the results that the developed QSAR classification model could conceivably be employed for further high-dimensional QSAR classification studies.

Matched MeSH terms: Quantitative Structure-Activity Relationship*

A new sulphated flavone and other phytoconstituents from the leaves of Tetracera indica Merr. and their alpha-glucosidase inhibitory activity

Alhassan AM, Ahmed QU, Latip J, Shah SAA

Nat Prod Res, 2019 Jan;33(1):1-8.

PMID: 29417849 DOI: 10.1080/14786419.2018.1437427

The bioactivity guided fractionation of Tetracera indica leaves crude ethanolic extract has afforded the isolation and characterization of six compounds including a new natural product viz., 5,7-dihydroxyflavone-O-8-sulphate (1) and five known flavonoids (2-6). The structures of the compounds were elucidated using 1D and 2D NMR and HRESIMS spectroscopic analyses. All the isolated compounds were evaluated for their in vitro inhibitory activity against alpha-glucosidase. Compound 1, 5 and 6 showed strong alpha-glucosidase inhibitory activity, 3 and 4 displayed weak activity while compound 2 was inactive. The interactions of the active compounds with alpha-glucosidase were further investigated using molecular docking to confirm their antidiabetic potential.

Matched MeSH terms: Structure-Activity Relationship

Fulltext A novel sequence-based predictor for identifying and characterizing thermophilic proteins using estimated propensity scores of dipeptides

Charoenkwan P, Chotpatiwetchkul W, Lee VS, Nantasenamat C, Shoombuatong W

Sci Rep, 2021 Dec 10;11(1):23782.

PMID: 34893688 DOI: 10.1038/s41598-021-03293-w

Owing to their ability to maintain a thermodynamically stable fold at extremely high temperatures, thermophilic proteins (TTPs) play a critical role in basic research and a variety of applications in the food industry. As a result, the development of computation models for rapidly and accurately identifying novel TTPs from a large number of uncharacterized protein sequences is desirable. In spite of existing computational models that have already been developed for characterizing thermophilic proteins, their performance and interpretability remain unsatisfactory. We present a novel sequence-based thermophilic protein predictor, termed SCMTPP, for improving model predictability and interpretability. First, an up-to-date and high-quality dataset consisting of 1853 TPPs and 3233 non-TPPs was compiled from published literature. Second, the SCMTPP predictor was created by combining the scoring card method (SCM) with estimated propensity scores of g-gap dipeptides. Benchmarking experiments revealed that SCMTPP had a cross-validation accuracy of 0.883, which was comparable to that of a support vector machine-based predictor (0.906-0.910) and 2-17% higher than that of commonly used machine learning models. Furthermore, SCMTPP outperformed the state-of-the-art approach (ThermoPred) on the independent test dataset, with accuracy and MCC of 0.865 and 0.731, respectively. Finally, the SCMTPP-derived propensity scores were used to elucidate the critical physicochemical properties for protein thermostability enhancement. In terms of interpretability and generalizability, comparative results showed that SCMTPP was effective for identifying and characterizing TPPs. We had implemented the proposed predictor as a user-friendly online web server at http://pmlabstack.pythonanywhere.com/SCMTPP in order to allow easy access to the model. SCMTPP is expected to be a powerful tool for facilitating community-wide efforts to identify TPPs on a large scale and guiding experimental characterization of TPPs.

Matched MeSH terms: Structure-Activity Relationship

A penalized quantitative structure-property relationship study on melting point of energetic carbocyclic nitroaromatic compounds using adaptive bridge penalty

Al-Fakih AM, Algamal ZY, Lee MH, Aziz M

SAR QSAR Environ Res, 2018 May;29(5):339-353.

PMID: 29493376 DOI: 10.1080/1062936X.2018.1439531

A penalized quantitative structure-property relationship (QSPR) model with adaptive bridge penalty for predicting the melting points of 92 energetic carbocyclic nitroaromatic compounds is proposed. To ensure the consistency of the descriptor selection of the proposed penalized adaptive bridge (PBridge), we proposed a ridge estimator ([Formula: see text]) as an initial weight in the adaptive bridge penalty. The Bayesian information criterion was applied to ensure the accurate selection of the tuning parameter ([Formula: see text]). The PBridge based model was internally and externally validated based on [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], the Y-randomization test, [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text] and the applicability domain. The validation results indicate that the model is robust and not due to chance correlation. The descriptor selection and prediction performance of PBridge for the training dataset outperforms the other methods used. PBridge shows the highest [Formula: see text] of 0.959, [Formula: see text] of 0.953, [Formula: see text] of 0.949 and [Formula: see text] of 0.959, and the lowest [Formula: see text] and [Formula: see text]. For the test dataset, PBridge shows a higher [Formula: see text] of 0.945 and [Formula: see text] of 0.948, and a lower [Formula: see text] and [Formula: see text], indicating its better prediction performance. The results clearly reveal that the proposed PBridge is useful for constructing reliable and robust QSPRs for predicting melting points prior to synthesizing new organic compounds.

Matched MeSH terms: Quantitative Structure-Activity Relationship*

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