Review on: quantitative structure activity relationship (QSAR) modeling

Repurposing Phytochemicals against Breast Cancer (MCF-7) using Classical Structure-Based Drug Design

BACKGROUND

The significant public health effect of breast cancer is demonstrated by its high global prevalence and the potential for severe health consequences. The suppression of the proliferative effects facilitated by the estrogen receptor alpha (ERα) in the MCF-7 cell line is significant for breast cancer therapy.

OBJECTIVE

The current work involves in-silico techniques for identifying potential inhibitors of ERα.

METHODS

The method combines QSAR models based on machine learning with molecular docking to identify potential binders for the ERα. Further, molecular dynamics simulation studied the stability of the complexes, and ADMET analysis validated the compound's properties.

RESULTS

Two compounds (162412 and 443440) showed significant binding affinities with ERα, with binding energies comparable to the established binder RL4. The ADMET qualities showed advantageous characteristics resembling pharmaceutical drugs. The stable binding of these ligands in the active region of ERα during dynamic conditions was confirmed by molecular dynamics simulations. RMSD plots and conformational stability supported the ligands' persistent occupancy in the protein's binding site. After simulation, two hydrogen bonds were found within the protein-ligand complexes of 162412 and 443440, with binding free energy values of -27.32 kcal/mol and -25.00 kcal/mol.

CONCLUSION

The study suggests that compounds 162412 and 443440 could be useful for developing innovative anti-ERα medicines. However, more research is needed to prove the compounds' breast cancer treatment efficacy. This will help develop new treatments for ERα-associated breast cancer.

AlphaFold Meets De Novo Drug Design: Leveraging Structural Protein Information in Multitarget Molecular Generative Models

Recent advancements in deep learning and generative models have significantly expanded the applications of virtual screening for drug-like compounds. Here, we introduce a multitarget transformer model, PCMol, that leverages the latent protein embeddings derived from AlphaFold2 as a means of conditioning a de novo generative model on different targets. Incorporating rich protein representations allows the model to capture their structural relationships, enabling the chemical space interpolation of active compounds and target-side generalization to new proteins based on embedding similarities. In this work, we benchmark against other existing target-conditioned transformer models to illustrate the validity of using AlphaFold protein representations over raw amino acid sequences. We show that low-dimensional projections of these protein embeddings cluster appropriately based on target families and that model performance declines when these representations are intentionally corrupted. We also show that the PCMol model generates diverse, potentially active molecules for a wide array of proteins, including those with sparse ligand bioactivity data. The generated compounds display higher similarity known active ligands of held-out targets and have comparable molecular docking scores while maintaining novelty. Additionally, we demonstrate the important role of data augmentation in bolstering the performance of generative models in low-data regimes. Software package and AlphaFold protein embeddings are freely available at https://github.com/CDDLeiden/PCMol.

Synthesis, biological evaluation, theoretical calculations, QSAR and molecular docking studies of novel arylaminonaphthols as potent antioxidants and BChE inhibitors

A completely green protocol was developed for the synthesis of a series of arylaminonaphthol derivatives in the presence of N-ethylethanolamine (NEEA) as a catalyst under ultrasonic irradiation and solventless conditions. The major assets of this methodology were the use of non-toxic organic medium, available catalyst, mild reaction condition, and good to excellent yield of desired products. All of the synthesized products were screened for their in vitro antioxidant activity using DPPH, ABTS, and Ferric-phenanthroline assays and it was found that most of them are potent antioxidant agents. Also, their butyrylcholinesterase inhibitory activity has been investigated in vitro. All tested compounds exhibited potential inhibitory activity toward BuChE when compared to standard reference drug galantamine, however, compounds 4r, 4u, 4 g and 4x gave higher butyrylcholinesterase inhibitory with IC50 values of 14.78 ± 0.65 µM, 16.18 ± 0.50 µM, 20.00 ± 0.50 µM, and 20.28 ± 0.08 µM respectively. On the other hand, we employed density functional theory (DFT), calculations to analyze molecular geometry and global reactivity descriptors, and MESP analysis to predict electrophilic and nucleophilic attacks. A quantitative structure-activity relationship (QSAR) investigation was conducted on the antioxidant and butyrylcholinesterase properties of 25 arylaminonaphthol derivatives, resulting in robust and satisfactory models. To evaluate their anti-Alzheimer's activity, compounds 4 g, 4q, 4r, 4u, and 4x underwent docking simulations at the active site of the acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), revealing why these compounds displayed superior activity, consistent with the biological findings.

Molecular structural modeling and physical characteristics of anti-breast cancer drugs via some novel topological descriptors and regression models

Research is continuously being pursued to treat cancer patients and prevent the disease by developing new medicines. However, experimental drug design and development is a costly, time-consuming, and challenging process. Alternatively, computational and mathematical techniques play an important role in optimally achieving this goal. Among these mathematical techniques, topological indices (TIs) have many applications in the drugs used for the treatment of breast cancer. TIs can be utilized to forecast the effectiveness of drugs by providing molecular structure information and related properties of the drugs. In addition, these can assist in the design and discovery of new drugs by providing insights into the structure-property/structure-activity relationships. In this article, a Quantitative Structure Property Relationship (QSPR) analysis is carried out using some novel degree-based molecular descriptors and regression models to predict various properties (such as boiling point, melting point, enthalpy, flashpoint, molar refraction, molar volume, and polarizability) of 14 drugs used for the breast cancer treatment. The molecular structures of these drugs are topologically modeled through vertex and edge partitioning techniques of graph theory, and then linear regression models are developed to correlate the computed values with the experimental properties of the drugs to investigate the performance of TIs in predicting these properties. The results confirmed the potential of the considered topological indices as a tool for drug discovery and design in the field of breast cancer treatment.

Predicting rejection of emerging contaminants through RO membrane filtration based on ANN-QSAR modeling approach: trends in molecular descriptors and structures towards rejections

In this work, a quantitative structure-activity relationship (QSAR) study was performed on a set of emerging contaminants (ECs) to predict their rejections by reverse osmosis membrane (RO). A wide range of molecular descriptors was calculated by Dragon software for 72 ECs. The QSAR data was analyzed by an artificial neural network method (ANN), in which four out of 3000 theoretical molecular descriptors were chosen and their significance was computed based on the Garson method. The significance trends of descriptors were as follows in descending order: ESpm14u > R2e > SIC1 > EEig03d. The selected descriptors were ranked based on their importance and then an explorative study was conducted on the QSAR data to show the trends in molecular descriptors and structures toward the rejections values of ECs. The MLR algorithm was used to make a linear model and the results were compared with those of the nonlinear ANN algorithm. The comparison results revealed it is necessary to apply the ANN model to this data with non-linear properties. For the whole dataset, the correlation coefficient (R2) and residual mean squared error (RMSE) of the ANN and MLR methods were 0.9528, 6.4224; and 0.8753, 11.3400, respectively. The comparison results showed the superiority of ANN modeling in the analysis of ECs' QSAR data.

Investigation of Potential Drug Targets for Cholesterol Regulation to Treat Alzheimer's Disease

Despite extensive research and seven approved drugs, the complex interplay of genes, proteins, and pathways in Alzheimer's disease remains a challenge. This implies the intricacies of the mechanism for Alzheimer's disease, which involves the interaction of hundreds of genes, proteins, and pathways. While the major hallmarks of Alzheimer's disease are the accumulation of amyloid plaques and tau protein tangles, excessive accumulation of cholesterol is reportedly correlated with Alzheimer's disease patients. In this work, protein-protein interaction analysis was conducted based upon the genes from a clinical database to identify the top protein targets with most data-indicated involvement in Alzheimer's disease, which include ABCA1, CYP46A1, BACE1, TREM2, GSK3B, and SREBP2. The reactions and pathways associated with these genes were thoroughly studied for their roles in regulating brain cholesterol biosynthesis, amyloid beta accumulation, and tau protein tangle formation. Existing clinical trials for each protein target were also investigated. The research indicated that the inhibition of SREBP2, BACE1, or GSK3B is beneficial to reduce cholesterol and amyloid beta accumulation, while the activation of ABCA1, CYP46A1, or TREM2 has similar effects. In this study, Sterol Regulatory Element-Binding Protein 2 (SREBP2) emerged as the primary protein target. SREBP2 serves a pivotal role in maintaining cholesterol balance, acting as a transcription factor that controls the expression of several enzymes pivotal for cholesterol biosynthesis. Novel studies suggest that SREBP2 performs a multifaceted role in Alzheimer's disease. The hyperactivity of SREBP2 may lead to heightened cholesterol biosynthesis, which suggested association with the pathogenesis of Alzheimer's disease. Lowering SREBP2 levels in an Alzheimer's disease mouse model results in reduced production of amyloid-beta, a major contributor to Alzheimer's disease progression. Moreover, its thoroughly analyzed crystal structure allows for computer-aided screening of potential inhibitors; SREBP2 is thus selected as a prospective drug target. While more protein targets can be added onto the list in the future, this work provides an overview of key proteins involved in the regulation of brain cholesterol biosynthesis that may be further investigated for Alzheimer's disease intervention.

Descriptor-free QSAR: effectiveness in screening for putative inhibitors of FGFR1

The long short-term memory (LSTM) algorithm has provided solutions to the limitations of the descriptors-utilizing QSAR models in drug design. However, the direct application of LSTM remains scarce. The effectiveness of a descriptor-free QSAR (LSTM-SM) in modeling the FGFR1 inhibitors dataset while comparing with two conventional QSAR using descriptors (126 bits Morgan fingerprint and 2 D descriptors respectively) as a baseline model was investigated in this study. The validated descriptor-free QSAR model was thereafter used to screen for active FGFR1 inhibitors in the ChemDiv database and subjected to molecular docking, induced-fit docking, QM-MM optimization, and molecular dynamics simulations to filter for compounds with high binding affinity and suggest the putative mechanism of inhibition and specificity. The LSTM-SM model performed better than conventional QSAR; having accuracy, specificity, and sensitivity of 0.92, model loss of 0.025, and AUC of 0.95. Fifteen thousand compounds were predicted as actives from the ChemDiv database and four compounds were finally selected. Of the four, two showed putatively effective binding interactions with key active site residues. Molecular dynamics simulations on these compounds in complex with the receptor further give insight into the conformational dynamics of each compound bounded to the receptor. The complexes formed are stable and exhibit a similar degree of compactness. Our findings predicted the advent of self-feature extracting machine learning algorithms of compounds, and have provided the possibility of better predictive model quality that is not necessarily limited by compound descriptors. The putative FGFR1 inhibitors, with their mechanism of inhibition and specificity, were elucidated using this approachCommunicated by Ramaswamy H. Sarma.

An in silico molecular modeling approach of halolactone derivatives as potential inhibitors for human immunodeficiency virus type-1 reverse transcriptase enzyme

Acquired Immune Deficiency Syndrome (AIDS) is an infectious disease caused by Human Immunodeficiency Virus (HIV) infection and its replication requires the Reverse Transcriptase (RT) enzyme. RT plays a key role in the HIV life cycle, making it one of the most important targets for designing new drugs. Thus, in order to increase therapeutic options against AIDS, halolactone derivatives (D-halolactone) that have been showed as potential non-nucleoside inhibitors of the RT enzyme were studied. In the present work, a series of D-halolactone were investigated by molecular modeling studies, combining Three-dimensional Quantitative Structure-Activity Relationship (3 D-QSAR), molecular docking and Molecular Dynamics (MD) techniques, to understand the molecular characteristics that promote biological activity. The internal and external validation parameters indicated that the 3 D-QSAR model has good predictive capacity and statistical significance. Contour maps provided useful information on the structural characteristics of compounds for anti-HIV-1 activity. The docking results showed that D-halolactone present good complementarity by the RT allosteric site. In MD simulations it was observed that the formation of enzyme-ligand complexes were favorable, and from the free energy decomposition it was found that Leu100, Val106, Tyr181, Try188, and Trp229 are key residues for stabilization in the enzymatic site. Thus, the results showed that the proposed models can be used to design promising HIV-1 RT inhibitors. Communicated by Ramaswamy H. Sarma.

Quantitative structure-activity relationship and machine learning studies of 2-thiazolylhydrazone derivatives with anti-Cryptococcus neoformans activity

Cryptococcus neoformans is a fungus responsible for infections in humans with a significant number of cases in immunosuppressed patients, mainly in underdeveloped countries. In this context, the thiazolylhydrazones are a promising class of compounds with activity against C. neoformans. The understanding of the structure-activity relationship of these derivatives could lead to the design of robust compounds that could be promising drug candidates for fungal infections. Specifically, modern techniques such as 4D-QSAR and machine learning methods were employed in this work to generate two QSAR models (one 2D and one 4D) with high predictive power (r² for the test set equals to 0.934 and 0.831, respectively), and one random forest classification model was reported with Matthews correlation coefficient equals to 1 and 0.62 for internal and external validations, respectively. The physicochemical interpretation of selected models, indicated the importance of aliphatic substituents at the hydrazone moiety to antifungal activity, corroborating experimental data.Communicated by Ramaswamy H. Sarma.

Quantitative structure-activity relationship modeling for predication of inhibition potencies of imatinib derivatives using SMILES attributes

Chronic myelogenous leukemia (CML) which is resulted from the BCR-ABL tyrosine kinase (TK) chimeric oncoprotein, is a malignant clonal disorder of hematopoietic stem cells. Imatinib is used as an inhibitor of BCR-ABL TK in the treatment of CML patients. The main object of the present manuscript is focused on constructing quantitative activity relationships (QSARs) models for the prediction of inhibition potencies of a large series of imatinib derivatives against BCR-ABL TK. Herren, the inbuilt Monte Carlo algorithm of CORAL software is employed to develop QSAR models. The SMILES notations of chemical structures are used to compute the descriptor of correlation weights (CWs). QSAR models are established using the balance of correlation method with the index of ideality of correlation (IIC). The data set of 306 molecules is randomly divided into three splits. In QSAR modeling, the numerical value of R², Q², and IIC for the validation set of splits 1 to 3 are in the range of 0.7180-0.7755, 0.6891-0.7561, and 0.4431-0.8611 respectively. The numerical result of [Formula: see text] > 0.5 for all three constructed models in the Y-randomization test validate the reliability of established models. The promoters of increase/decrease for pIC₅₀ are recognized and used for the mechanistic interpretation of structural attributes.

A new perspective on the modeling and topological characterization of H-Naphtalenic nanosheets with applications

In the past few years, two-dimensional (2D) layered nanomaterials have greatly attracted the scientific community. Among 2D nanomaterials, the porphyrin-based Naphtalenic nanosheets have been the subject of intense research due to their utilization in photo-dynamic therapy and nanodevices. New technologies based on nanomaterials or Naphtalenic nanosheet are advantageous in overcoming the problems in conventional drug delivery like poor solubility, toxicity and poor release pattern of drugs. In chemical network theory, various molecular descriptors are used to predict the chemical properties of molecules; these molecular descriptors are found to be very useful for Quantitative Structure-Activity/ Quantitative Structure-Property (QSAR/QSPR) relationship analysis in materials engineering, chemical and pharmaceutical industries. Researchers have computed the molecular descriptors for various nanostructures; however, despite intense research, the topology of nanostructures is not yet well understood. Specially, to our knowledge, the computation of topological indices for the line graph of subdivision graph of H-Naphtalenic nanosheet has not been discussed so far, which may open new perspectives for a more accurate and reliable topological characterization of this nanosheet.In this article, we employed some important degree-based topological indices to study the chemical structure of Naphtalenic nanosheet as a chemical network for QSAR/QSPR analysis. We have computed these degree-based topological indices for the line graph of subdivision graph of H-Naphtalenic nanosheet and derived formulas for them. Based on the derived formulas, numerical results are obtained and the physical and chemical properties of the under study nanosheet are investigated.

NNAIMQ: A neural network model for predicting QTAIM charges

Atomic charges provide crucial information about the electronic structure of a molecular system. Among the different definitions of these descriptors, the one proposed by the Quantum Theory of Atoms in Molecules (QTAIM) is particularly attractive given its invariance against orbital transformations although the computational cost associated with their calculation limits its applicability. Given that Machine Learning (ML) techniques have been shown to accelerate orders of magnitude the computation of a number of quantum mechanical observables, in this work, we take advantage of ML knowledge to develop an intuitive and fast neural network model (NNAIMQ) for the computation of QTAIM charges for C, H, O, and N atoms with high accuracy. Our model has been trained and tested using data from quantum chemical calculations in more than 45 000 molecular environments of the near-equilibrium CHON chemical space. The reliability and performance of NNAIMQ have been analyzed in a variety of scenarios, from equilibrium geometries to molecular dynamics simulations. Altogether, NNAIMQ yields remarkably small prediction errors, well below the 0.03 electron limit in the general case, while accelerating the calculation of QTAIM charges by several orders of magnitude.

Predicting zebrafish (Danio rerio) embryo developmental toxicity through a non-conformational QSAR approach

For many years, the frequent use of synthetic chemicals in the manufacture of veterinary drugs and plague control products has raised negative effects on human health and other non-target organisms, promoting the need to employ a practical and suitable methodology for early risk identification of several thousand commercial compounds. The zebrafish (Danio rerio) embryo has been emerged as one sustainable animal model for measuring developmental toxicity, an endpoint that is included in the regulatory procedures to approve chemicals, avoiding conventional and costly toxicity assays based on animal testing. In this context, the Quantitative Structure-Activity Relationships (QSAR) theory is applied to develop a predictive model based on a well-defined zebrafish embryo developmental toxicity database reported by the ToxCast™ Phase I chemical library of the Environmental Protection Agency (U.S. EPA). By means of four freely available softwares, a set with 28,038 non-conformational descriptors that encode the largest amount of permanent structural features are readily calculated. The Replacement Method (RM) variable subset selection technique provided the best regression models. Thereby, a linear QSAR model with proper statistical quality (R_train² = 0.64, RMSE_train = 0.49) is established in agreement with the Organization for Economic Co-operation and Development principles, accomplishing each internal (loo, l15 % o, VIF and Y-randomization) and external (R_test²,R_m², Q_F1², Q_F2², Q_F3² and CCC) validation criterion. The present QSAR approach provides a useful computational tool to estimate zebrafish developmental toxicity of new, untasted or hypothetical compounds, and it can contribute to the general lack of QSAR models in the literature to predict this endpoint.

QSAR Modelling of Peptidomimetic Derivatives towards HKU4-CoV 3CLpro Inhibitors against MERS-CoV

In this paper, we report the relationship between the anti-MERS-CoV activities of the HKU4 derived peptides for some peptidomimetic compounds and various descriptors using the quantitative structure activity relationships (QSAR) methods. The used descriptors were computed using ChemSketch, Marvin Sketch and ChemOffice software. The principal components analysis (PCA) and the multiple linear regression (MLR) methods were used to propose a model with reliable predictive capacity. The original data set of 41 peptidomimetic derivatives was randomly divided into training and test sets of 34 and 7 compounds, respectively. The predictive ability of the best MLR model was assessed by determination coefficient R2 = 0.691, cross-validation parameter Q2cv = 0.528 and the external validation parameter R2test = 0.794.

Thorough evaluation of OECD principles in modelling of 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine derivatives using QSARINS

The human immunodeficiency virus is a lethal pathology considered as a worldwide problem. The search for new strategies for the treatment of this disease continues to be a great challenge in the scientific community. In this study, a series of 107 derivatives of 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine, previously evaluated experimentally against HIV-I reverse transcriptase, was used to model antiretroviral activity. A model of linear regression, implemented in the QSARINS software, was developed with a genetic algorithm for variable selection. The fit of its parameters was good and exhaustive validation, according to the OECD regulatory principles, was performed. Also, the applicability domain was established. In addition, its robustness (r ² = 0.84), stability (Q ² _LOO = 0.81; Q ² _LMO = 0.80) and good predictive power (r ² _EXT = 0.85) is proved. So, it was used to predict the antiretroviral activity of eight compounds obtained by rational drug design. Finally, it can be affirmed that the proposed tools allow the rapid and economic identification of potential antiretroviral drugs.

Recommender Systems in Antiviral Drug Discovery

Recommender systems (RSs), which underwent rapid development and had an enormous impact on e-commerce, have the potential to become useful tools for drug discovery. In this paper, we applied RS methods for the prediction of the antiviral activity class (active/inactive) for compounds extracted from ChEMBL. Two main RS approaches were applied: collaborative filtering (Surprise implementation) and content-based filtering (sparse-group inductive matrix completion (SGIMC) method). The effectiveness of RS approaches was investigated for prediction of antiviral activity classes ("interactions") for compounds and viruses, for which some of their interactions with other viruses or compounds are known, and for prediction of interaction profiles for new compounds. Both approaches achieved relatively good prediction quality for binary classification of individual interactions and compound profiles, as quantified by cross-validation and external validation receiver operating characteristic (ROC) score >0.9. Thus, even simple recommender systems may serve as an effective tool in antiviral drug discovery.

Quantum chemical predictions of water-octanol partition coefficients applied to the SAMPL6 logP blind challenge

Theoretical approaches for predicting physicochemical properties are valuable tools for accelerating the drug discovery process. In this work, quantum chemical methods are used to predict water-octanol partition coefficients as a part of the SAMPL6 blind challenge. The SMD continuum solvent model was employed with MP2 and eight DFT functionals in conjunction with correlation consistent basis sets to determine the water-octanol transfer free energy. Several tactics towards improving the predictions of the partition coefficient were examined, including increasing the quality of basis sets, considering tautomerization, and accounting for inhomogeneities in the water and n-octanol phases. Evaluation of these various schemes highlights the impact of modeling approaches across different methods. With the inclusion of tautomers and adjustments to the permittivity constants, the best predictions were obtained with smaller basis sets and the O3LYP functional, which yielded an RMSE of 0.79 logP units. The results presented correspond to the SAMPL6 logP submission IDs: DYXBT, O7DJK, and AHMTF.

Peptidic Antifreeze Materials: Prospects and Challenges

Necessitated by the subzero temperatures and seasonal exposure to ice, various organisms have developed a remarkably effective means to survive the harsh climate of their natural habitats. Their ice-binding (glyco)proteins keep the nucleation and growth of ice crystals in check by recognizing and binding to specific ice crystal faces, which arrests further ice growth and inhibits ice recrystallization (IRI). Inspired by the success of this adaptive strategy, various approaches have been proposed over the past decades to engineer materials that harness these cryoprotective features. In this review we discuss the prospects and challenges associated with these advances focusing in particular on peptidic antifreeze materials both identical and akin to natural ice-binding proteins (IBPs). We address the latest advances in their design, synthesis, characterization and application in preservation of biologics and foods. Particular attention is devoted to insights in structure-activity relations culminating in the synthesis of de novo peptide analogues. These are sequences that resemble but are not identical to naturally occurring IBPs. We also draw attention to impactful developments in solid-phase peptide synthesis and 'greener' synthesis routes, which may aid to overcome one of the major bottlenecks in the translation of this technology: unavailability of large quantities of low-cost antifreeze materials with excellent IRI activity at (sub)micromolar concentrations.