Virtual Combinatorial Chemistry and Pharmacological Screening: A Short Guide to Drug Design.

Traditionally, drug development involved the individual synthesis and biological evaluation of hundreds to thousands of compounds with the intention of highlighting their biological activity, selectivity, and bioavailability, as well as their low toxicity. On average, this process of new drug development involved, in addition to high economic costs, a period of several years before hopefully finding a drug with suitable characteristics to drive its commercialization. Therefore, the chemical synthesis of new compounds became the limiting step in the process of searching for or optimizing leads for new drug development. This need for large chemical libraries led to the birth of high-throughput synthesis methods and combinatorial chemistry. Virtual combinatorial chemistry is based on the same principle as real chemistry-many different compounds can be generated from a few building blocks at once. The difference lies in its speed, as millions of compounds can be produced in a few seconds. On the other hand, many virtual screening methods, such as QSAR (Quantitative Sturcture-Activity Relationship), pharmacophore models, and molecular docking, have been developed to study these libraries. These models allow for the selection of molecules to be synthesized and tested with a high probability of success. The virtual combinatorial chemistry-virtual screening tandem has become a fundamental tool in the process of searching for and developing a drug, as it allows the process to be accelerated with extraordinary economic savings.

Molecular Topology for the Search of New Anti-MRSA Compounds.

The variability of methicillin-resistant Staphylococcus aureus (MRSA), its rapid adaptive response against environmental changes, and its continued acquisition of antibiotic resistance determinants have made it commonplace in hospitals, where it causes the problem of multidrug resistance. In this study, we used molecular topology to develop several discriminant equations capable of classifying compounds according to their anti-MRSA activity. Topological indices were used as structural descriptors and their relationship with anti-MRSA activity was determined by applying linear discriminant analysis (LDA) on a group of quinolones and quinolone-like compounds. Four extra equations were constructed, named DFMRSA1, DFMRSA2, DFMRSA3 and DFMRSA4 (DFMRSA was built in a previous study), all with good statistical parameters, such as Fisher-Snedecor F (>68 in all cases), Wilk's lambda (<0.13 in all cases), and percentage of correct classification (>94% in all cases), which allows a reliable extrapolation prediction of antibacterial activity in any organic compound. The results obtained clearly reveal the high efficiency of combining molecular topology with LDA for the prediction of anti-MRSA activity.

Synthesis of Quinolones and Zwitterionic Quinolonate Derivatives with Broad-Spectrum Antibiotic Activity.

Quinolones are one of the most extensively used therapeutic families of antibiotics. However, the increase in antibiotic-resistant bacteria has rendered many of the available compounds useless. After applying our prediction model of activity against E. coli to a library of 1000 quinolones, two quinolones were selected to be synthesized. Additionally, a series of zwitterionic quinolonates were also synthesized. Quinolones and zwitterionic quinolonates were obtained by coupling the corresponding amine with reagent 1 in acetonitrile. Antibacterial activity was assessed using a microdilution method. All the compounds presented antibacterial activity, especially quinolones 2 and 3, selected by the prediction model, which had broad-spectrum activity. Furthermore, a new type of zwitterionic quinolonate with antibacterial activity was found. These compounds can lead to a new line of antimicrobials, as the structures, and, therefore, their properties, are easily adjustable in the amine in position 4 of the pyridine ring.

New Pharmacokinetic and Microbiological Prediction Equations to Be Used as Models for the Search of Antibacterial Drugs.

Currently, the development of resistance of Enterobacteriaceae bacteria is one of the most important health problems worldwide. Consequently, there is a growing urge for finding new compounds with antibacterial activity. Furthermore, it is very important to find antibacterial compounds with a good pharmacokinetic profile too, which will lead to more efficient and safer drugs. In this work, we have mathematically described a series of antibacterial quinolones by means of molecular topology. We have used molecular descriptors and related them to various pharmacological properties by using multilinear regression (MLR) analysis. The regression functions selected by presenting the best combination of a number of quality and validation metrics allowed for the reliable prediction of clearance (CL), and minimum inhibitory concentration 50 against Enterobacter aerogenes (MIC50Ea) and Proteus mirabilis (MIC50Pm). The obtained results clearly reveal that the combination of molecular topology methods and MLR provides an excellent tool for the prediction of pharmacokinetic properties and microbiological activities in both new and existing compounds with different pharmacological activities.

Tree-Based QSAR Model for Drug Repurposing in the Discovery of New Antibacterial Compounds Against Escherichia coli.

Drug repurposing appears as an increasing popular tool in the search of new treatment options against bacteria. In this paper, a tree-based classification method using Linear Discriminant Analysis (LDA) and discrete indexes was used to create a QSAR (Quantitative Structure-Activity Relationship) model to predict antibacterial activity against Escherichia coli. The model consists on a hierarchical decision tree in which a discrete index is used to divide compounds into groups according to their values for said index in order to construct probability spaces. The second step consists in the calculation of a discriminant function which determines the prediction of the model. The model was used to screen the DrugBank database, identifying 134 drugs as possible antibacterial candidates. Out of these 134 drugs, 8 were antibacterial drugs, 67 were drugs approved for different pathologies and 55 were drugs in experimental stages. This methodology has proven to be a viable alternative to the traditional methods used to obtain prediction models based on LDA and its application provides interesting new drug candidates to be studied as repurposed antibacterial treatments. Furthermore, the topological indexes Nclass and Numhba have proven to have the ability to group active compounds effectively, which suggests a close relationship between them and the antibacterial activity of compounds against E. coli.

Molecular Topology for the Discovery of New Broad-Spectrum Antibacterial Drugs.

In this study, molecular topology was used to develop several discriminant equations capable of classifying compounds according to their antibacterial activity. Topological indices were used as structural descriptors and their relation to antibacterial activity was determined by applying linear discriminant analysis (LDA) on a group of quinolones and quinolone-like compounds. Four equations were constructed, named DF1, DF2, DF3, and DF4, all with good statistical parameters such as Fisher-Snedecor's F (over 25 in all cases), Wilk's lambda (below 0.36 in all cases) and percentage of correct classification (over 80% in all cases), which allows a reliable extrapolation prediction of antibacterial activity in any organic compound. From the four discriminant functions, it can be extracted that the presence of sp3 carbons, ramifications, and secondary amine groups in a molecule enhance antibacterial activity, whereas the presence of 5-member rings, sp2 carbons, and sp2 oxygens hinder it. The results obtained clearly reveal the high efficiency of combining molecular topology with LDA for the prediction of antibacterial activity.

New solvent options for in vivo assays in the Galleria mellonella larvae model.

Experimentation in mammals is a long and expensive process in which ethical aspects must be considered, which has led the scientific community to develop alternative models such as that of Galleria mellonella. This model is a cost and time effective option to act as a filter in the drug discovery process. The main limitation of this model is the lack of variety in the solvents used to administer compounds, which limits the compounds that can be studied using this model. Five aqueous (DMSO, MeOH, acetic acid, HCl and NaOH) and four non-aqueous (olive oil, isopropyl myristate, benzyl benzoate and ethyl oleate) solvents was assessed to be used as vehicles for toxicity and antimicrobial activity in vivo assays. All the tested solvents were innocuous at the tested concentrations except for NaOH, which can be used at a maximum concentration of 0.5 M. The toxicity of two additional compounds, 5-aminosalicylic acid and DDT, was also assessed. The results obtained allow for the testing of a broader range of compounds using wax moth larvae. This model appears as an alternative to mammal models, by acting as a filter in the drug development process and reducing costs and time invested in new drugs.

Topological index Nclass as a factor determining the antibacterial activity of quinolones against Escherichia coli.

Aim: Due to antibiotic resistance and the lack of investment in antimicrobial R&D, quantitative structure-activity relationship (SAR) methods appear as an ideal approach for the discovery of new antibiotics. Result & methodology: Molecular topology and linear discriminant analysis were used to construct a model to predict activity against Escherichia coli. This model establishes new SARs, of which, molecular size and complexity (Nclass), stand out for their discriminant power. This model was used for the virtual screening of the Index Merck database, with results showing a high success rate as well as a moderate restriction. Conclusion: The model efficiently finds new active compounds. The topological index Nclass can act as a filter in other quantitative structure-activity relationship models predicting activity against E. coli.

Obtaining Microbiological and Pharmacokinetic Highly Predictive Equations.

In this paper, a Multilinear Regression (MLR) analysis has been carried out in order to accurately predict physicochemical properties and biological activities of a group of antibacterial quinolones by means of a set of structural descriptors called topological indices. The aim of this work is to develop prediction equations for these properties after collecting the maximum number of data from the literature on antibacterial quinolones. The five regression functions selected by presenting the best combination of various statistical parameters, subsequently validated by means of internal validation (intercorrelation, Y-randomization and leave-one-out cross-validation tests), allowed the reliable prediction of minimum inhibitory concentration 50 versus Staphylococcus aureus (MIC50Sa), Streptococcus pyogenes (MIC50Spy) and Bacteroides fragilis (MIC50Bf), Mean Residence Time (MRT) after oral administration and volume of distribution (VD). We conclude that the combination of molecular topology methods and MLR provides an excellent tool for the prediction of pharmacological properties.

Topological pattern for the search of new active drugs against methicillin resistant Staphylococcus aureus.

Molecular topology was used to develop a mathematical model capable of classifying compounds according to antimicrobial activity against methicillin resistant Staphylococcus aureus (MRSA). Topological indices were used as structural descriptors and their relation to antimicrobial activity was determined by using linear discriminant analysis. This topological model establishes new structure activity relationships which show that the presence of cyclopropyl, chlorine and ramification pairs at a distance of two bonds favor this activity, while the presence of tertiary amines decreases it. This model was applied to a combinatorial library of a thousand and one 6-fluoroquinolones, from which 117 theoretical active molecules were obtained. The compound 10 and five new quinolones were tested against MRSA. They all showed some activity against MRSA, although compounds 6, 8 and 9 showed anti-MRSA activity similar to ciprofloxacin. This model was also applied to 263 theoretical antibacterial agents described by us in a previous work, from which 34 were predicted as theoretically active. Anti-MRSA activity was found bibliographically in 9 of them (ensuring at least 26% of success), and from the rest, 3 compounds were randomly chosen and tested, finding mitomycin C to be more active than ciprofloxacin. The results demonstrate the utility of the molecular topology approaches for identifying new drugs active against MRSA.

Application of a mathematical topological pattern of antihistaminic activity for the selection of new drug candidates and pharmacology assays.

Molecular topology was used to achieve a mathematical model capable of classifying compounds according to their antihistaminic activity and low sedative effects. By application of this model of activity to databases containing chemical reagents and drugs exhibiting other pharmacological activity, we selected 30 compounds with possible antihistaminic activity. After those with possible sedative effects were discarded, activity tests were performed with five chemical reagents and three drugs searching for in vivo antihistaminic activity. The obtained results indicate that compounds such as 4-[(E)-2-(1,3-benzothiazol-2-yl)vinyl]-N,N-dimethylaniline (AH2), 2-ethyl-9,10-dimethoxyanthracene (AH4), and 2,4-bis(alpha,alpha-dimethylbenzyl)phenol (AH5) showed antihistaminic activity above terfenadine, the reference drug, whereas others, for instance, pergolide, miconazole, trihexyphenidyl, 2-(dibenzylamino-3-phenyl-1-propanol (AH1), and N-benzylquininium chloride (AH3), were less active than terfenadine.

New potential antihistaminic compounds. Virtual combinatorial chemistry, computational screening, real synthesis, and pharmacological evaluation.

To study the utility of the virtual combinatorial chemistry coupled with computational screening, a library of amine and urea derivatives was designed by virtual combinatorial synthesis and eventually computationally screened by a mathematical topological model as antihistaminic compounds. The results reveal that virtual combinatorial synthesis and virtual screening together with molecular topology are a powerful tool in the design of new drugs.

Topological Model for the Search of New Antibacterial Drugs. 158 Theoretical Candidates.

In this paper, molecular topology was used to develop a mathematical model capable of classifying compounds according to their antibacterial activity. Topological indices were used as structural descriptors and their relation to antibacterial activity was determined by applying linear discriminant analysis (LDA) on a group of quinolones, widely used nowadays because of their broad spectrum of activity, well tolerance profile and advantageous pharmacokinetic properties. The topological model of activity obtained included two discriminant functions, selected by a combination of various statistical paremeters such as Fisher-Snedecor F and Wilk's lambda, and allows the reliable prediction of antibacterial activity in any organic compound. After a virtual pharmacological screening on a library of 6375 compounds, the model has selected 263 as active compounds, from which 40% have proven antibacterial activity. The results obtained clearly reveal the high efficiency of molecular topology for the prediction of pharmacological activities. These models are very helpful in the discovery of new applications of natural and synthetic molecules with different chemical or biological properties. Therefore, we finally present 158 strong candidates to be developed as novel antibacterials.