On a topological interpretation of electronic and vibrational molecular energies

Abstract A relationship between Randic's connectivity index and various quantum mechanical parameters derived from the Huckel Molecular Orbital (HMO) approach is demonstrated. When applied to conjugated hydrocarbons, this index represents the measure of the global π electron molecular energy and, therefore, of the resonance energy. Moreover, the development of the procedure, allows the introduction of a new definition of the bond order which, in turn, makes possible a better prediction not only for bond lengths of naphtalene but also for the resonance integral and conjugation energy for butadiene. Also, a corrected value for the Randic index is deduced, which allows for the reduction of the…

New bronchodilators selected by molecular topology.

Molecular topology has been applied to find new lead compounds with bronchodilator activity. Among the selected compounds stands out 3-(1H-tetrazol-5yl)-9H-thioxanthene-9 -one-10,10-dioxide, anthrarobin, 9-oxo-9H-thioxantene-3-carboxylic-10,10-dioxide acid, acenocoumarol and griseofulvin, with a percentage of relaxation, at 0.1 mM, of 91, 92, 85, 69, and 74%, respectively. Theophylline shows a correspondent value of 77% (Emax = 100% at 1 mM).

Anti- Toxoplasma Activities of 24 Quinolones and Fluoroquinolones In Vitro: Prediction of Activity by Molecular Topology and Virtual Computational Techniques

ABSTRACT The apicoplast, a plastid-like organelle of Toxoplasma gondii , is thought to be a unique drug target for quinolones. In this study, we assessed the in vitro activity of quinolones against T. gondii and developed new quantitative structure-activity relationship models able to predict this activity. The anti- Toxoplasma activities of 24 quinolones were examined by means of linear discriminant analysis (LDA) using topological indices as structural descriptors. In parallel, in vitro 50% inhibitory concentrations (IC 50 s) were determined in tissue culture. A multilinear regression (MLR) analysis was then performed to establish a model capable of classifying quinolones by in vitro acti…

Computational Methods in Developing Quantitative Structure-Activity Relationships (QSAR): A Review

Virtual filtering and screening of combinatorial libraries have recently gained attention as methods complementing the high-throughput screening and combinatorial chemistry. These chemoinformatic techniques rely heavily on quantitative structure-activity relationship (QSAR) analysis, a field with established methodology and successful history. In this review, we discuss the computational methods for building QSAR models. We start with outlining their usefulness in high-throughput screening and identifying the general scheme of a QSAR model. Following, we focus on the methodologies in constructing three main components of QSAR model, namely the methods for describing the molecular structure …

Alzheimer: A Decade of Drug Design. Why Molecular Topology can be an Extra Edge?

Background The last decade was characterized by a growing awareness about the severity of dementia in the field of age-related and no age-related diseases and about the importance to invest resources in the research of new, effective treatments. Among the dementias, Alzheimer's plays a substantial role because of its extremely high incidence and fatality. Several pharmacological strategies have been tried but still now, Alzheimer keeps being an untreatable disease. In literature, the number of QSAR related drug design attempts about new treatments for Alzheimer is huge, but only few results can be considered noteworthy. Providing a detailed analysis of the actual situation and reporting the…

Stoichiometric and kinetic study of the 99Tc-DMSA complex obtained with stannous excess: A possible model for the physico-chemical behaviour of the radiopharmaceutical 99mTc-DMSA

A stoichiometric and kinetic study was made of the 99mTc-DMSA complex obtained in the presence of large amounts of Sn2+. It is demonstrated that the Tc oxidation state is 3+. It is established that the complex degrades to another one if there is an Sn2+ deficiency. These results were confirmed by spectroscopic and spectrophotometric methods.

Discovery of new antimalarial compounds by use of molecular connectivity techniques.

Abstract Molecular connectivity has been applied to the search for new compounds with antimalarial activity. Linear discriminant analysis and connectivity functions were used to select several potentially suitable drugs which were tested for antimalarial properties by use of an in-vitro micro test which estimates parasite growth by measurement of incorporation of [3H]hypoxanthine. Hexetidine stands out among the compounds selected. Activity assays were performed with Plasmodium falciparum passou and 3CD7 strains, for which the IC50 values (doses resulting in 50% inhibition) were 320 and 400 ng mL−1 respectively. These results are comparable with those obtained for quinine chlorhydrate (IC50…

Synthesis, biological evaluation and chemometric analysis of indazole derivatives. 1,2-Disubstituted 5-nitroindazolinones, new prototypes of antichagasic drug

Chagas disease chemotherapy, currently based on only two drugs, nifurtimox and benznidazole, is far from satisfactory and therefore the development of new antichagasic compounds remains an important goal. On the basis of antichagasic properties previously described for some 1,2-disubstituted 5-nitroindazolin-3- ones (21, 33) and in order to initiate the optimization of activity of this kind of compounds, we have prepared a series of related analogs (22-32, 34-38, 58 and 59) and tested in vitro these products against epimastigote forms of Trypanosoma cruzi. 2-Benzyl-1-propyl (22), 2-benzyl-1-isopropyl (23) and 2-benzyl-1-butyl (24) derivatives have shown high trypanocidal activity and low un…

Event-based criteria in GT-STAF information indices: theory, exploratory diversity analysis and QSPR applications

Versatile event-based approaches for the definition of novel information theory-based indices (IFIs) are presented. An event in this context is the criterion followed in the "discovery" of molecular substructures, which in turn serve as basis for the construction of the generalized incidence and relations frequency matrices, Q and F, respectively. From the resultant F, Shannon's, mutual, conditional and joint entropy-based IFIs are computed. In previous reports, an event named connected subgraphs was presented. The present study is an extension of this notion, in which we introduce other events, namely: terminal paths, vertex path incidence, quantum subgraphs, walks of length k, Sach's subg…

Molecular Search of New Active Drugs AgainstToxoplasma Gondii

Molecular connectivity has been applied to the search of new compounds with activity against the protozoan Toxoplasma gondii, using a stepwise linear discriminant analysis (SLDA) which is able to classify a compound according its activity either as active or as inactive. Among the selected compounds, andrographolide and dibenzotiophene sulfone stand out, both with IC50 values lower than 1 microgram/ml, which are comparable to these of drugs such as sulfamethoxazole, pyrimethamine and trimethoprim, with IC50 values equal to 1.1, 0.04 and 2.31 micrograms/ml, respectively. These results confirm the usefulness of our topological approach for the selection and design of new-lead drugs active aga…

Application of molecular topology to the prediction of potency and selection of novel insecticides active against malaria vectors

Abstract A study on the basis of molecular topology has been carried out to predict the potency of insecticides active against malaria vectors (Culex) as well as to select novel compounds potentially active on those vectors. The results, performed over two sets of compounds, namely hormone-like and ‘common’ or wide-spectra insecticides, demonstrate that the adequate combination of topological charge indices and simple topological-geometric indices, yield very good results in both, the prediction of potency and the selection of new insecticides. Further development should be addressed in the future; however, the achievement described here is extremely encouraging.

Drugs Repurposing for Coronavirus Treatment: Computational Study Based On Molecular Topology

The present communication illustrates the results of a computational study based on molecular topology, focused on the repositioning of drugs to treat the SARS-CoV-2 virus, better known as coronavirus, responsible for the COVID-19 disease. Using lopinavir, a well-known viral protease inhibitor as the reference drug, a mathematical pattern is found allowing the screening of the market drugs, searching for potential candidates to inhibit the said enzyme. This way new possible therapeutic alternatives to fight the coronavirus are found. Results indicate that antivirals such as brecanavir, as well as various groups of drugs, among which are antibiotics of the macrolide family (azithromycin, cla…

Application of molecular topology in the prediction of new compounds with anti-trypanosomal cytotoxic activity

La enfermedad de Chagas es una antropozoonosis parasitaria de transmisión mayoritariamente vectorial. Si bien afecta principalmente a América, constituye una de las mayores enfermedades desatendidas a nivel mundial. Solamente dos fármacos con un alto grado de toxicidad se encuentran disponibles para su tratamiento, por lo que es preciso aunar esfuerzos en pos del desarrollo de nuevas drogas antitripanosomales eficaces y con escasos efectos adversos. En este estudio, se aplicó la topología molecular para el desarrollo de un modelo QSAR capaz de predecir la actividad citotóxica antitripanosomal de un grupo de 39 compuestos. El modelo desarrollado mediante análisis lineal discriminante permiti…

Chemistry Explained by Topology: An Alternative Approach

Molecular topology can be considered an application of graph theory in which the molecular structure is characterized through a set of graph-theoretical descriptors called topological indices. Molecular topology has found applications in many different fields, particularly in biology, chemistry, and pharmacology. The first topological index was introduced by H. Wiener in 1947 [1]. Although its very first application was the prediction of the boiling points of the alkanes, the Wiener index has demonstrated since then a predictive capability far beyond that. Along with the Wiener index, in this paper we focus on a few pioneering topological indices, just to illustrate the connection between p…

Predictability and prediction of lowest observed adverse effect levels in a structurally heterogeneous set of chemicals

A database of chronic lowest observed adverse effect levels (LOAELs) for 234 compounds, previously compiled from different sources (Toxicology Letters79, 131-143 (1995)), was modelled using graph theoretical descriptors. This study reveals that data are not homogeneous. Only those data originating from the U.S. Environmental Protection Agency (EPA) reports could be well modelled by multilinear regression (MLR) and linear discriminant analysis (LDA). In contrast, data available from the specific procedures of the National Toxicology Program (NTP) database introduced noise and did not render good models either alone, or in combination with the EPA data.

Getting new bronchodilator compounds from molecular topology.

Abstract Molecular topology has been used to select new lead bronchodilator compounds. The main advantage of this method, as compared to others frequently used, is that it does not require a previous explicit knowledge of the mechanism of action (MOA) of the compounds analyzed. A large database (12,000 chemicals) has been examined in this study to find less than 5% compounds with bronchodilator activity. After removing those compounds already described as bronchodilators, we present here the results for 20 among these compounds, some of them showing other pharmacological activities. Some of the compounds selected in this study showed higher relaxation and higher potency than theophylline, w…

What place does molecular topology have in today’s drug discovery?

Introduction: Most methods in molecular and drug design are currently based on physicochemical descriptors. However, molecular topology, which relies on topological descriptors, has also shown value for molecular design even if it does not take into account the physical or chemical properties of ligands and receptors, including the ligand-receptor interaction itself. Areas covered: Herein, the authors provide new insights into the importance of molecular topology according to some of the latest discoveries in physics and chemistry. Furthermore, the authors report on the most significant achievements in drug design using molecular topology over the last 5 years and give their expert perspect…

Biodegradability Prediction of Fragrant Molecules by Molecular Topology

Biodegradability is a key property in the development of safer fragrances. In this work we present a green methodology for its preliminary assessment. The structure of various fragrant molecules is characterized by computing a large set of topological indices. Those relevant to biodegradability are selected by means of a hybrid stepwise selection method to build a linear classifier. This model is compared with a more complex artificial neural network trained with the indices previously found. After validation, the models show promise for time and cost reduction in the development of new, safer fragrances. The methodology presented could easily be adapted to many quasi-big data problems in R…

Molecular topology applied to the discovery of 1-benzyl-2-(3-fluorophenyl)-4-hydroxy-3-(3-phenylpropanoyl)-2H-pyrrole-5-one as a non-ligand-binding-pocket antiandrogen

We report the discovery of 1-benzyl-2-(3- fluorophenyl)-4-hydroxy-3-(3-phenylpropanoyl)-2H-pyrrole- 5-one as a novel non-ligand binding pocket (non-LBP) antagonist of the androgen receptor (AR) through the application of molecular topology techniques. This compound, validated through time-resolved fluorescence resonance energy transfer and fluorescence polarization biological assays, provides the basis for lead optimization and structure−activity relationship analysis of a new series of non-LBP AR antagonists. Induced-fit docking and molecular dynamics studies have been performed to establish a consistent hypothesis for the interaction of the new active molecule on the AR surface. Refereed/…

Getting discriminant functions of antibacterial activity from physicochemical and topological parameters.

Linear discriminant analysis has been demonstrated to be a very useful tool in the selection and design of new drugs. Up to now we have used it through the search of a topological pattern of activity. In this work our goal is to calculate a complete set of physicochemical parameters using semiempirical (quantum chemical) calculations as well as topological indices (TIs) and try to find out any discriminant function for antibacterial activity through the combined use of both types of descriptors. The physicochemical parameters, such as heat of formation, HOMO, LUMO, dipole moment, polarizability, hyperpolarizability, PM3 generated IR vibrational frequencies, etc., were calculated using PM3 H…

How Molecular Topology Can Help in Amyotrophic Lateral Sclerosis (ALS) Drug Development: A Revolutionary Paradigm for a Merciless Disease

r Abstract: Even if amyotrophic lateral sclerosis is still considered an orphan disease to date, its prevalence among the population is growing fast. Despite the efforts made by researchers and pharmaceutical companies, the cryptic information related to the biological and physiological onset mechanisms, as well as the complexity in identifying specific pharmacological targets, make it almost impossible to find effective treatments. Furthermore, because of complex ethical and economic aspects, it is usually hard to find all the necessary resources when searching for drugs for new orphan diseases. In this context, computational methods, based either on receptors or ligands, share the capabil…

In vitro activity of linezolid, clarithromycin and moxifloxacin against clinical isolates of Mycobacterium kansasii

To compare the activity of linezolid with a range of drugs used in the treatment of Mycobacterium kansasii infections.The percentages of resistant isolates against isoniazid, rifampicin and ethambutol were 2.9%, 1.9% and 2.9%, respectively. All isolates were susceptible to clarithromycin and moxifloxacin both with MIC(90) values of 0.125 mg/L. Linezolid was active against all isolates with MIC(50) and MIC(90) values of 0.5 and 1 mg/L, respectively, both below the susceptibility breakpoint established for mycobacteria.Linezolid, clarithromycin or moxifloxacin, could be used as alternative drugs for treatment of infections due to rifampicin-resistant isolates as well as short-course or interm…

Aplicación de la topología molecular a la predicción de la actividad antimalárica de análogos de la 4-anilinoquinolina

La malaria es una enfermedad parasitaria causada por protozoos del género Plasmodium y transmitida por vectores del género Anopheles . En 2019 esta enfermedad se cobró la vida de más de 400.000 personas, de las cuales un 94 % se concentraban en la región de África. Uno de los principales problemas en el control de la malaria es la aparición de resistencias frente a los diferentes fármacos que existen, es por ello que es necesario el desarrollo de alternativas antimaláricas eficaces. En este estudio se ha aplicado la topología molecular a una serie de compuestos análogos de la 4-anilinoquinolina con actividad inhibitoria de la proliferación de 3 cepas de Plasmodium falciparum, una sensibl…

Virtual Combinatorial Syntheses and Computational Screening of New Potential Anti-Herpes Compounds

The activity of new anti-HSV-1 chemical structures, designed by virtual combinatorial chemical synthesis and selected by a computational screening, is determined by an in vitro assay. A virtual library of phenol esters and anilides was formed from two databases of building blocks: one with carbonyl fragments and the other containing both substituted phenoxy and phenylamino fragments. The library of virtually assembled compounds was computationally screened, and those compounds which were selected by our mathematical model as active ones were finally synthesized and tested. Our antiviral activity model is a "tandem" of four linear functions of topological graph-theoretical descriptors. A giv…

Topological Approach to Analgesia

Topological Approach to Drug Design

In this paper we demonstrated that by an adequate combination of different topological indices it is possible to select and design new active compounds in different therapeutical scopes, with a very high efficiency level. Particularly successful in the search of new "lead drugs", the results show the surprising ability of the topological methods to describe molecular structures.

Topological virtual screening: a way to find new anticonvulsant drugs from chemical diversity.

A topological virtual screening (tvs) test is presented, which is capable of identifying new drug leaders with anticonvulsant activity. Molecular structures of both anticonvulsant-active and non active compounds, extracted from the Merck Index database, were represented using topological indexes. By means of the application of a linear discriminant analysis to both sets of structures, a topological anticonvulsant model (tam) was obtained, which defines a connectivity function. On the basis of this model, 41 new structures with anticonvulsant activity have been identified by a topological virtual screening.

New agents active against Mycobacterium avium complex selected by molecular topology: a virtual screening method

Objectives: In order to select new drugs and to predict their in vitro activity against Mycobacterium avium complex (MAC), new quantitative structure-activity relationship (QSAR) models were developed. Methods: The activities against MAC of 29 structurally heterogeneous drugs were examined by means of linear discriminant analysis (LDA) and multilinear regression analysis (MLRA) by using topological indices (TI) as structural descriptors. In vitro antimycobacterial activities were determined by a broth microdilution method with 7H9 medium. Results: The topological model obtained successfully classifies over 80% of compounds as active or inactive; consequently, it was applied in the search fo…

New antifungals selected by molecular topology.

Abstract Molecular topology has been applied to find the new lead antimycotic compounds. Among the selected compounds stands out 3,3′-(4,4′ - Biphenylene)bis(2,5-diphenyl-2H-tetrazolium chloride), Benztropine mesylate and Dicyclopentamethylenethiuram disulphide, with minimum inhibitory concentrations between 1.6 and 2 μg / mL.

New Analgesics Designed by Molecular Topology

Molecular topology has been applied to the design of new analgesic drugs, utilizing linear discriminant analysis and connectivity functions using different topological descriptors. Of a total of 26 compounds selected, 17 showed analgesic activity. The following stood out particularly, showing analgesic values greater than 75% regarding ASA (acetylsalicylic acid), the reference drug: 2-(1-propenyl)phenol, 2′4′ dimethylacetophenone, p-chlorobenzohydrazide, 1-(p-chlorophenyl) propanol and 4-benzoyl-3-methyl-1-phenyl-2-pyrazolin-5-one. The usefulness of the design method has been demonstrated in the search of new chemical structures having analgesic effects, some of which could become “lead dru…

Computer-guided drug repurposing: Identification of trypanocidal activity of clofazimine, benidipine and saquinavir

In spite of remarkable advances in the knowledge on Trypanosoma cruzi biology, no medications to treat Chagas disease have been approved in the last 40 years and almost 8 million people remain infected. Since the public sector and non-profit organizations play a significant role in the research efforts on Chagas disease, it is important to implement research strategies that promote translation of basic research into the clinical practice. Recent international public-private initiatives address the potential of drug repositioning (i.e. finding second or further medical uses for known-medications) which can substantially improve the success at clinical trials and the innovation in the pharmac…

Molecular connectivity to find β-blockers with low toxicity

Abstract Molecular connectivity has been used to find new β-blocker drugs using linear discriminant analysis and connectivity functions with different topological descriptors. Among the selected compounds stands out the probucol and the β-carotene. Both of them interact with β adrenoceptors.

Molecular Topology QSAR Strategy for Crop Protection: New Natural Fungicides with Chitin Inhibitory Activity

Nowadays, crop protection is a major concern and how to proceed is a delicate point of contention. New products must be safe and ecofriendly in accordance with the actual legislation. In this context, we present a quantitative structure-activity relationship strategy based on molecular topology as a tool for generating natural products as potential fungicides following a mechanism of action based on the synthesis of chitin inhibition (chitinase inhibition). Two discriminant equations using statistical linear discriminant analysis were used to identify three potential candidates (1-methylxanthine, hematommic acid, and antheraxanthin). The equations showed accuracy and specificity levels abov…

Search of Chemical Scaffolds for Novel Antituberculosis Agents

3 A method to identify chemical scaffolds potentially active against Mycobacterium tuberculosis is presented. The molecular features of a set of structurally heterogeneous antituberculosis drugs were coded by means of structural invariants. Three tech- niques were used to obtain equations able to model the antituberculosis activity: linear discriminant analysis, multilinear re- gression, and shrinkage estimation-ridge regression. The model obtained was statistically validated through leave-n-out test, and an external set and was applied to a database for the search of new active agents. The selected compounds were assayed in vitro, and among those identified as active stand reserpine, N,N,N…

Aplicación de la topología molecular para la predicción de biodegradación anaerobia de clorofenoles

Se ha aplicado la topología molecular y el análisis de regresión multilineal en la búsqueda de un modelo de relación cuantitativa estructura-actividad (QSAR) capaz de predecir la capacidad de biodegradación anaerobia de un grupo de clorofenoles. Tomando el valor de la constante de velocidad de desaparición del derivado clorofenolico, log k, como variable dependiente y los descriptores topológicos como variables independientes, se obtuvo una ecuación con tres variables y coeficientes de correlación y de predicción , R2=0.9291 y Q2=0.870. El modelo fue validado a través de una validación interna y un test de aleatoriedad. Los resultados obtenidos muestran una alta capacidad de predicción para…

Novel Cancer Chemotherapy Hits by Molecular Topology: Dual Akt and Beta-Catenin Inhibitors

Background and purposeColorectal and prostate cancers are two of the most common types and cause of a high rate of deaths worldwide. Therefore, any strategy to stop or at least slacken the development and progression of malignant cells is an important therapeutic choice. The aim of the present work is the identification of novel cancer chemotherapy agents. Nowadays, many different drug discovery approaches are available, but this paper focuses on Molecular Topology, which has already demonstrated its extraordinary efficacy in this field, particularly in the identification of new hit and lead compounds against cancer. This methodology uses the graph theoretical formalism to numerically chara…

A Graph-Theoretical Approach to Calculate Vibrational Energies of Atomic and Subatomic Systems

One of the challenges still pending in string theory and other particle physics related fields is the accurate prediction of the masses of the elementary particles defined in the standard model. In this paper an original algorithm to assign graphs to each of these particles is proposed. Based on this mapping, we demonstrate that certain indices associated with the topology of the graph (graph theoretical indices) are very effective in predicting the masses of the particles. Specifically, the spectral moments of the graph adjacency matrix weighted by edge degrees play a key role in the excellent correlations found. Moreover, the same topological pattern is found in other well known quantum s…

Prediction of acute toxicity of organophosphorus pesticides using topological indices

Topological indices were used in the prediction of the acute toxicity (intraperitoneal and oral LD(50)) of organophosphorus pesticides on rats. Models with six variables for the prediction of LD(50)-i.p. (r = 0.849, Q(2) = 0.613) and eight variables for LD(50)-oral (r = 0.906, Q(2) = 0.701) were selected. External group and cross-validation by use of leave-n-out tests were also performed in order to assess the stability and the prediction performance of the selected topological models.

Molecular topology as a novel approach for drug discovery

Molecular topology (MT) has emerged in recent years as a powerful approach for the in silico generation of new drugs. One key part of MT is that, in the process of drug design/discovery, there is no need for an explicit knowledge of a drug's mechanism of action unlike other drug discovery methods.In this review, the authors introduce the topic by explaining briefly the most common methodology used today in drug design/discovery and address the most important concepts of MT and the methodology followed (QSAR equations, LDA, etc.). Furthermore, the significant results achieved, from this approach, are outlined and discussed.The results outlined herein can be explained by considering that MT r…

Application of molecular topology to the prediction of antifungal activity for a set of dication-substituted carbazoles, furans and benzimidazoles

In this paper, the endpoint is the application of molecular topology to the search of QSAR relations into a group of dicationsubstituted carbazoles, furans and benzimidazoles, all showing antifungal activity against C. albicans. Mathematical and statistical methods such as linear regression and discriminant analysis, are used to goal. The obtained results clearly show a high efficiency of the formalism on the prediction and classification of antifungal activity. 83% of the compounds showing MIC , 10 mg/ml (active group) are correctly classified, whilst 100% overall accuracy is achieved for those compounds showing MIC . 100 mg/ml (inactive group). q 2003 Elsevier Science B.V. All rights rese…

Application of Molecular Topology to the Prediction of the Reaction Yield and Anticancer Activity of Imidazole and Guanidine Derivatives

In this study molecular topology based QSAR has been applied to predict the reaction yield and anticancer activity of 18 imidazole and guanidine derivatives. Four properties were evaluated, namely reaction yield, anti prostatic-cancer activity, anti breast-cancer activity and anti lung-cancer activity. The four models have been validated by both internal and cross validation, and also by randomness tests. The results obtained are in full agreement with the experimental results and confirm the precision, accuracy and robustness of the method followed. After carrying out a virtual screening upon such models, new imidazole and guanidine derivatives with potential anticancer activity are propos…

Application of Molecular Topology for the Prediction of Reaction Yields and Anti-Inflammatory Activity of Heterocyclic Amidine Derivatives

Topological-mathematical models based on multiple linear regression analyses have been built to predict the reaction yields and the anti-inflammatory activity of a set of heterocylic amidine derivatives, synthesized under environmental friendly conditions, using microwave irradiation. Two models with three variables each were selected. The models were validated by cross-validation and randomization tests. The final outcome demonstrates a good agreement between the predicted and experimental results, confirming the robustness of the method. These models also enabled the screening of virtual libraries for new amidine derivatives predicted to show higher values of reaction yields and anti-infl…

Application of molecular topology to the prediction of the antimalarial activity of a group of uracil-based acyclic and deoxyuridine compounds.

A topological-mathematical model has been arranged to search for new derivatives of deoxyuridine and related compounds acting as antimalarials against Plasmodium falciparum. By using linear discriminant and multilinear regression analysis a model with two functions was capable to predict adequately the IC(50) for each compound of the training and test series. After carrying out a virtual screening based upon such a model, new structures potentially active against P. falciparum are proposed.

Molecular topology: A new strategy for antimicrobial resistance control

The control of antimicrobial resistance (AMR) seems to have come to an impasse. The use and abuse of antibacterial drugs has had major consequences on the genetic mutability of both pathogenic and nonpathogenic microorganisms, leading to the development of new highly resistant strains. Because of the complexity of this situation, an in silico strategy based on QSAR molecular topology was devised to identify synthetic molecules as antimicrobial agents not susceptible to one or several mechanisms of resistance such as: biofilms formation (BF), ionophore (IA) activity, epimerase (EI) activity or SOS system (RecA inhibition). After selecting a group of 19 compounds, five of them showed signific…

Application of Molecular Topology to the Prediction of Water Quality Indices of Alkylphenol Pollutants

In this paper, topological-mathematical models based on multilineal regression analysis have been built as a model of the degradability of 26 alkylphenols through the Chemical Oxygen Demand (COD) and Biochemical Oxigen Demand (BOD5). Two models with three-variable were selected (r2= 0.8793 and q2=0.8075 for log(1/COD) and r2= 0.8928 and q2=0.8327 for log(1/BOD5). The models were validated by cross-validation, internal validation and randomization tests. The results, which stand in good accordance with the obtained results, confirm the robustness of the method.

Prediction of properties of chiral compounds by molecular topology

Abstract A common assumption in chemistry is that chiral behavior is associated with 3-D geometry. However, chiral information is related to symmetry, which allows the topological handling of chiral atoms by weighted graphs and the calculation of new descriptors that give a weight to the corresponding entry in the main diagonal of the topological matrix. In this study, it is demonstrated that, operating in this way, chiral topological indices are obtained that can differentiate the pharmacological activity between pairs of enantiomers. The 50% inhibitory concentration (IC50) values of the D2 dopamine receptor and the σ receptor for a group of 3-hydroxy phenyl piperidines are specifically pr…

Search of a topological pattern to evaluate toxicity of heterogeneous compounds.

Abstract Molecular connectivity has been applied to the search of mathematical models able to predict the carcinogenic and teratogenic activity of a wide group of structurally heterogeneous compounds. Through the linear discriminant analysis and the diagrams of distribution of pharmacological activity, the classification criteria that minimizes the percentage of error are established. The easiness and speed of the calculation of the descriptors used in this work make the models developed useful in data bases containing a huge number of compounds.

General topological patterns of known drugs.

Abstract Discriminating “drug-like” from “non-drug-like” compounds is a relatively emerging topic within the drug research. The basic assumption is that it is possible to obtain relevant information from structural features common to the known drugs, in order to discard a huge number of candidate chemical structures with low probability of becoming drugs. A graph-theoretical contribution to this subject is reported in this paper, by making exclusive use of linear relationships. The results suggest that it is possible to achieve a pattern of general pharmacological activity based on molecular topology. Conclusions are tentative pending verification of the results with larger compound librari…

Search for New Antihistaminic Compounds by Molecular Connectivity

In this paper it is demonstrated that by adequate selection of topological descriptors we can make possible the prediction of different pharmacological properties, such as plasmatic concentration or sedative effect, within a group of antihistaminic drugs. Moreover, also demonstrated is the usefulness of molecular connectivity in the search of new active compounds. Examples of such compounds are 4-(l-buthylpenthyl)pyridine, N-(3-bromopropyl)-phtalimide and N-(3-chlorpropyl)-piperidin hydrochloride. All of them show antihistaminic activity values more than 30% higher than that of terfenadine, which is used as the reference drug.

Modeling Drug-Induced Anorexia by Molecular Topology

Molecular topology (MT) has demonstrated to be a very good technique for describing molecular structures and to predict physical, chemical, and biological properties of compounds. In this paper, a topological-mathematical model based on MT has been developed for identifying drug compounds showing anorexia as a side effect. An external validation (test set) has been carried out, yielding over an 80% correct classification in the active and inactive compounds. These results reinforce the role of MT as a potential useful tool for predicting drug side effects.

Latest advances in molecular topology applications for drug discovery

Molecular topology (MT) has emerged in recent years as a powerful approach for the in silico generation of new drugs. In the last decade, its application has become more and more popular among the leading research groups in the field of quantitative structure-activity relationships (QSAR) and drug design. This has, in turn, contributed to the rapid development of new techniques and applications of MT in QSAR studies, as well as the introduction of new topological indices.This review collates the main innovative techniques in the field of MT and provides a description of the novel topological indices recently introduced, through an exhaustive recompilation of the most significant works carri…

Molecular topology - dissimilar similarities.

The present paper depicts the role of molecular topology in the study of similarity–dissimilarity between molecular structures. It proves that molecular topology represents a very useful tool for getting common patterns of pharmacological activity and hence an efficient approach for the search of novel lead drugs.

Structural invariants for the prediction of relative toxicities of polychloro dibenzo-p-dioxins and dibenzofurans

Multivariate models are reported that can predict the relative toxicity of compounds with severe environmental impact, namely polychloro dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs). Multiple linear regression analysis (MLR) and partial least square projections of latent variables (PLS) show the usefulness of graph-theoretical descriptors, mainly topological charge indices (TCIs), in these series. The general trends of the group are correctly reproduced and better results are presented than have previously been published. In general, the more toxic compounds exhibit more symmetric molecular structures.

Some Relationships between Molecular Energy-Topology and Symmetry

Molecular Topology (M.T.) has demonstrated its efficiency in the prediction of many experimental parameters. The application of the topological indices to the prediction of pharmacological properties, and, above all, to its inverse problem, the drug design, is particularly interesting [1,2]. Several attempts to explain the reasons of such efficiency have been carried out [3,4]. So far, we are not close to a definitive answer.

QSAR methods for the discovery of new inflammatory bowel disease drugs

Inflammatory bowel disease (IBD) represents an important class of chronic gastrointestinal tract disease. And although there are already several useful treatments to reduce and control the symptoms, there is still no cure. One drug discovery technique used is the computer-aided (in silico) discovery approach which has largely demonstrated efficacy. Computational techniques, when used in combination with traditional drug discovery methodology, greatly increase the chance of drug discovery in a sustainable and economical fashion.This review aims to provide the most recent and important advances of in silico IBD drug discovery. While this review is mainly focused on QSAR methods, especially th…

Improving the local vertex invariants in alkane graphs through a standard molecular orbital approach

Abstract In this work, novel topological indices are introduced by the application of algorithms based on molecular orbital theory. Actually, the novel indices are obtained by computing new values of the local vertex invariants (LOVIs) in alkane graphs. The most significant result is the dramatic increase in the predictive capability achieved with the topological charge indices weighted according the new LOVIs’ values in the prediction of four key properties in the set of octane isomers, namely heat of atomization, molar refraction, heat of vaporization and boiling point.

Identification of New Templates for the Synthesis of BEA, BEC, and ISV Zeolites Using Molecular Topology and Monte Carlo Techniques

The presence of organic structure directing agents (templates) in the synthesis of zeolites allows the synthesis to be directed, in many cases, toward structures in which there is a large stabilization between the template and the zeolite micropore due to dispersion interactions. Although other factors are also important (temperature, pH, Si/Al ratio, etc.), systems with strong zeolite-template interactions are good candidates for an application of new computational algorithms, for instance those based in molecular topology (MT), that can be used in combination with large databases of organic molecules. Computational design of new templates allows the synthesis of existing and new zeolites …

Application de la topologie moléculaire à la prédiction de la viscosité liquide des composés organiques

Nous avons applique la topologie moleculaire a la recherche d'un modele mathematique capable de predire la viscosite liquide d'un large groupe de composes organiques contenant C, H, O, N, S et des halogenes. Les descripteurs topologiques utilises pour cette etude des relations quantitatives structure-propiete, R.Q.S.P., sont les indices de connectivite de Kier et Hall -jusqu'a l'ordre quatre- ainsi que les indices atomiques electrotopologiques. La qualite de l'equation de regression multilineaire obtenue (aussi dite « fonction de connectivite») a ete evaluee par une etude de validation croisee. Tous les composes excepte le 1,1,2-trichlorotrifluorethane s'ajustent au modele propose.

Molecular topology as novel strategy for discovery of drugs with aβ lowering and anti-aggregation dual activities for Alzheimer's disease.

Background and Purpose: In this study, we demonstrate the use of Molecular topology (MT) in an Alzheimer's disease (AD) drug discovery program. MT uses and expands upon the principles governing the molecular connectivity theory of numerically characterizing molecular structures, in the present case, active anti-AD drugs/agents, using topological descriptors to build models. Topological characterization has been shown to embody sufficient molecular information to provide strong correlation to therapeutic efficacy. Experimental Approach: We used MT to include multiple bioactive properties that allows for the identification of multifunctional single agent compounds, in this case, the dual func…

On the contribution of molecular topology to drug design and discovery.

Abstract The role of molecular topology (MT) in the design and selection of new drugs is discussed. After an overview of the different in silico molecular design current technologies, the QSAR analysis is dealt in detail with particular emphasis in the use of topological indices as molecular descriptors. The results of the application of MT in drug design and discovery are described and finally a possible explanation is given about some of the key reasons explaining it's the extraordinary performance.

Water-Hydrophobic Zeolite Systems

Water intrusion-extrusion in hydrophobic microporous AFI, IFR, MTW and TON pure silica zeolites (zeosils) has been investigated through molecular dynamics (MD) simulations. It was found that intruded water volumes correlate with the free volume of the zeosil unit cells. Calculated adsorption isotherms allowed us to estimate the amounts of water intruded, and deviations from experiments (lower experimental with respect to calculated intrusion pressures) have been;explained in terms of connectivity defects in the synthesized materials. Water phase transitions in defectless zeosils occur in a narrow range at high pressure. On the basis of a simple model, we derived a thermodynamic equation tha…

Prediction of quinolone activity against Mycobacterium avium by molecular topology and virtual computational screening.

ABSTRACT We conducted a quantitative structure-activity relationship study using a database of 158 quinolones previously tested against Mycobacterium avium-M. intracellulare complex in order to develop a model capable of predicting the activity of new quinolones against the M. avium-M. intracellulare complex in vitro. Topological indices were used as structural descriptors and were related to anti- M. avium-M. intracellulare complex activity by using the linear discriminant analysis (LDA) statistical technique. The discriminant equation thus obtained correctly classified 137 of the 158 quinolones, including 37 of a test group of 44 randomly chosen compounds. This model was then applied to 2…

Application of molecular topology for the prediction of the reaction times and yields under solvent-free conditions

Ball milling and conventional magnetic stirring can be used to support different laboratory techniques with a highly efficient mixing of reagents under solvent-free conditions. By using multilinear regression and linear discriminant analysis, topological-mathematical models have been built to predict the yield and the reaction time for organocatalytic reactions, Suzuki reactions and reactions of synthesis of heterocyclic compounds. The results from the in silico predictions confirm the usefulness of the approach followed.

QSAR multi-target in drug discovery: a review.

The main purpose of the present review is to summarize the most significant works up to date in the field of multi-target QSAR (mt-QSAR), in order to emphasize the importance that this technique has acquired over the last decade. Unlike traditional QSAR techniques, mt-QSAR permits to calculate the probability of activity of a given compound against different biological or pharmacological targets. In simple terms, a single equation for multiple outputs. To emphasize more the importance of the mt-QSAR in the field of drug discovery, we also present a novel mt-QSAR model, made on purpose by our research group, for the prediction of the susceptibility of Gram + and Gram - anaerobic bacteria.

New hypoglycaemic agents selected by molecular topology.

Abstract New compounds showing hypoglycaemic activity have been designed through a computer aided method based on quantitative structure–activity relationship (QSAR) and molecular connectivity. After calculation of topological indices for a set of 89 compounds including active and inactive with regards to hypoglycaemic action, linear discriminant analysis was performed so that a useful model to predict such an activity was achieved. Later on, the discriminant model was applied on a huge database so that fourteen compounds were selected as potential new hypoglycaemics. From them, just five were finally selected for experimental test on expected hypoglycaemic activity. Among the selected comp…

P2‐511: From in silico to in vitro to in vivo: ‐ Novel approach in Alzheimer's disease drug discovery

Computational analysis of macrolides as SARS-CoV-2 main protease inhibitors: a pattern recognition study based on molecular topology and validated by molecular docking

Since the outbreak of the current SARS-CoV-2 pandemic, much has been discussed about the effectiveness of treatments based on hydroxychloroquine combined with azithromycin or another macrolide. However, few articles have dealt with the possibility of using macrolides alone in treating the disease. In the present article, the authors' hypothesis centers on the possibility that macrolides are effective against SARS-CoV-2 by inhibiting the virus protease. In support of this hypothesis, significant results are collected by following an in silico strategy based on a combination of molecular topology and docking. The results are in accordance with recent clinical data generated during the pandemi…

Labelling of DMSA with 99Tc without exogenous reducing agents

Advances in the molecular modeling and quantitative structure–activity relationship-based design for antihistamines

Nowadays the use of antihistamines (AH) is increasing steadily. These drugs are able to act on a variety of pathological conditions of the organism. A number of computer-aided (in silico) approaches have been developed to discover and develop novel AH drugs. Among these methods stand the ones based on drug-receptor docking, thermodynamics, as well as the quantitative structure-activity relationships (QSAR).This review collates the most recent advances in the use of computer approaches for the search and characterization of novel AH drugs. Within the QSAR methods, particular attention will be paid to those based on molecular topology (MT) because of their demonstrated efficacy in discovering…

ChemInform Abstract: Getting Discriminant Functions of Antibacterial Activity from Physicochemical and Topological Parameters.

Linear discriminant analysis has been demonstrated to be a very useful tool in the selection and design of new drugs. Up to now we have used it through the search of a topological pattern of activity. In this work our goal is to calculate a complete set of physicochemical parameters using semiempirical (quantum chemical) calculations as well as topological indices (TIs) and try to find out any discriminant function for antibacterial activity through the combined use of both types of descriptors. The physicochemical parameters, such as heat of formation, HOMO, LUMO, dipole moment, polarizability, hyperpolarizability, PM3 generated IR vibrational frequencies, etc., were calculated using PM3 H…

Pharmacological studies of 1-(p-chlorophenyl)propanol and 2-(1-hydroxy-3-butenyl)phenol: Two new non-narcotic analgesics designed by molecular connectivity

Abstract Molecular topology has been applied to the design of new analgesic drugs. Linear discriminant analysis and connectivity functions were used to design two potentially suitable drugs which were synthesized and tested for analgesic properties by the acetic acid-induced abdominal constriction test in mice and the tail-flick test in rats. In mice, the compound 1-(p-chlorophenyl)propanol showed higher analgesic activity, both intraperitoneally and orally, than acetylsalicylic acid. 2-(1-Hydroxy-3-butenyl)phenol exhibited a lesser protective effect (70% of that shown by acetylsalicylic acid). In rats, acetylsalicylic acid gave the greatest protection against pain when administered intrape…

Introduction to molecular topology: basic concepts and application to drug design.

In this review it is dealt the use of molecular topology (MT) in the selection and design of new drugs. After an introduction of the actual methods used for drug design, the basic concepts of MT are defined, including examples of calculation of topological indices, which are numerical descriptors of molecular structures. The goal is making this calculation familiar to the potential students and allowing a straightforward comprehension of the topic. Finally, the achievements obtained in this field are detailed, so that the reader can figure out the great interest of this approach.

Molecular topology: a useful tool for the search of new antibacterials.

Molecular topology has been applied to find new lead antibacterial compounds. Among the selected compounds, hesperidin, neohesperidin and Mordant Brown 24 stand out, with minimum inhibitory concentrations 90, MIC90<0.3 mg / mL.

New active drugs against liver stages of Plasmodium predicted by molecular topology.

ABSTRACT We conducted a quantitative structure-activity relationship (QSAR) study based on a database of 127 compounds previously tested against the liver stage of Plasmodium yoelii in order to develop a model capable of predicting the in vitro antimalarial activities of new compounds. Topological indices were used as structural descriptors, and their relation to antimalarial activity was determined by using linear discriminant analysis. A topological model consisting of two discriminant functions was created. The first function discriminated between active and inactive compounds, and the second identified the most active among the active compounds. The model was then applied sequentially t…

Prediction of Molecular Volume and Surface of Alkanes by Molecular Topology.

Molecular volume and molecular surface are expressed as a function of topological degree in alkane graphs. This allows not only a straightforward approach to calculate such physicochemical magnitudes but also an interpretation of the role of the local vertex invariant (LOVI) or valence degree, delta, as well as the connectivity indices in the prediction of physicochemical properties. The interpretation is based on the concept of molecular accessibility (as introduced by Estrada, J. Phys. Chem. A 2002, 106, 9085) for which precise mathematical definitions are provided.

DesMol2, an Effective Tool for the Construction of Molecular Libraries and Its Application to QSAR Using Molecular Topology

A web application, DesMol2, which offers two main functionalities, is presented: the construction of molecular libraries and the calculation of topological indices. These functionalities are explained through a practical example of research of active molecules to the formylpeptide receptor (FPR), a receptor associated with chronic inflammation in systemic amyloidosis and Alzheimer&rsquo

New Anti-Neoplastics Obtained by a Molecular Connectivity Method

Molecular Connectivity is a method, which allows to discriminate different pharmacological activities on the basics of numeric parameters of the molecules in study, related with specific and exclusive indexes. In the present study, we propose two potentially anti-neoplasic compounds: tricromil and zomepirac, by analyzing more than a hundred different chemicals.

Use of molecular topology for the prediction of physico-chemical, pharmacokinetic and toxicological properties of a group of antihistaminic drugs

We used molecular connectivity to search mathematical models for predicting physico-chemical (e.g. the partition coefficient, P), pharmacokinetic (e.g. the time of maximum plasma level, and toxicological properties (lethal dose, LD) for a group of antihistaminic drugs. The results obtained clearly reveal the high efficiency of molecular topology for the prediction of these properties. Randomization and cross-validation by use of leave-one-out tests were also performed in order to assess the stability and the prediction ability of the connectivity functions selected.

New cytostatic agents obtained by molecular topology

Abstract Four new cytostatic compounds have been obtained by computer aided selection based on Molecular Connectivity, a topological approach to molecular structural study. Three of them, namely tetracycline, doxycycline and piromidic acid are well known antibiotic agents, and the fourth, carminic acid, is an innocuous colorant. Although no previous report of activity was found, on the used cell lines, for any of the selected compounds, carminic acid may be considered a new lead one since no structure-related cytostatic molecules have been reported in the literature. These results are interesting for two reasons: First, new potential low-toxicity anticancer drugs show to be a possible thera…

Pharmacological distribution diagrams: a tool for de novo drug design.

Abstract Discriminant analysis applied to SAR studies using topological descriptors allows us to plot frequency distribution diagrams: a function of the number of drugs within an interval of values of discriminant function vs. these values. We make use of these representations, pharmacological distribution diagrams (PDDs), in structurally heterogeneous groups where generally they adopt skewed Gaussian shapes or present several maxima. The maxima afford intervals of discrimianant function in which exists a good expectancy to find new active drugs. A set of β-blockers with contrasted activity has been selected to test the ability of PDDs as a visualizing technique, for the identification of n…