Structure –Activity Relationships by Autocorrelation Descriptors and Genetic Algorithms

2011 ◽  
pp. 60-94 ◽  
Author(s):  
Viviana Consonni ◽  
Roberto Todeschini
Keyword(s):  
Molecular Structure ◽  
Molecular Descriptors ◽  
Biological Activities ◽  
Chemical Properties ◽  
Structural Features ◽  
Point Of View ◽  
Structure Activity Relationships ◽  
Structure Activity ◽  
Similarity Relationships ◽  
Definition Of

Quantitative Structure-Activity Relationships (QSARs) are models relating variation of molecule properties, such as biological activities, to variation of some structural features of chemical compounds. Three main topics take part of the QSAR/QSPR approach to the scientific research: the representation of molecular structure, the definition of molecular descriptors and the chemoinformatics tools. Molecular descriptors are numerical indices encoding some information related to the molecular structure. They can be both experimental physico-chemical properties of molecules and theoretical indices calculated by mathematical formulas or computational algorithms. In the last few decades, much interest has been addressed to studying how to encompass and convert the information encoded in the molecular structure into one or more numbers used to establish quantitative relationships between structures and properties, biological activities or other experimental properties. Autocorrelation descriptors are a class of molecular descriptors based on the statistical concept of spatial autocorrelation applied to the molecular structure. The objective of this chapter is to investigate the chemical information encompassed by autocorrelation descriptors and elucidate their role in QSAR and drug design. After a short introduction to molecular descriptors from a historical point of view, the chapter will focus on reviewing the different types of autocorrelation descriptors proposed in the literature so far. Then, some methodological topics related to multivariate data analysis will be overviewed paying particular attention to analysis of similarity/diversity of chemical spaces and feature selection for multiple linear regressions. The last part of the chapter will deal with application of autocorrelation descriptors to study similarity relationships of a set of flavonoids and establish QSARs for predicting affinity constants, Ki, to the GABAA benzodiazepine receptor site, BzR.

The History and Development of Quantitative Structure-Activity Relationships (QSARs)

2017 ◽  
Vol 2 (2) ◽  
pp. 36-46 ◽  
Author(s):  
John C. Dearden
Keyword(s):  
Molecular Structure ◽  
Biological Activity ◽  
Molecular Descriptors ◽  
Biological Activities ◽  
Molecular Size ◽  
Liquid Viscosity ◽  
Quantitative Structure ◽  
Structure Activity ◽  
The Subject ◽  
Quantitative Structure Activity Relationships

Following the publication of the history and development of QSAR, it became apparent that a number of matters had not been covered. This addendum is an attempt to rectify that. A very early approach (ca. 60 B.C.) by Lucretius shows that he understood how molecular size and complexity affect liquid viscosity. Comments by Kant (1724-1804) emphasized the necessity of mathematics in science. A claim that the work of von Bibra and Harless in 1847 pre-dated that of Overton and H.H. Meyer is shown not to be correct. K.H. Meyer and Gottlieb-Billroth published in 1920 what is probably the first QSAR equation. Brown, who with his co-author Fraser is credited with the first definitive recognition in 1868-9 that biological activity is a function of molecular structure, is often cited as Crum Brown; in fact, Crum was his second given name. The QSAR work of the Soviet chemist N.V. Lazarev in the 1940s was far ahead of his time, showing numerous correlations of biological activities and physicochemical properties with molecular descriptors. The subject of inverse QSAR is discussed.

scholarly journals Potential of Steroidal Alkaloids in Cancer: Perspective Insight Into Structure–Activity Relationships

2021 ◽  
Vol 11 ◽  
Author(s):  
Ying Huang ◽  
Gen Li ◽  
Chong Hong ◽  
Xia Zheng ◽  
Haiyang Yu ◽  
...  
Keyword(s):  
Chemical Structure ◽  
Structural Modification ◽  
Biological Activities ◽  
Chemical Properties ◽  
Steroidal Alkaloids ◽  
Pharmacological Activities ◽  
Structure Activity Relationships ◽  
Lead Compounds ◽  
Structure Activity ◽  
Insight Into

Steroidal alkaloids contain both steroidal and alkaloid properties in terms of chemical properties and pharmacological activities. Due to outstanding biological activities such as alkaloids and similar pharmacological effects to other steroids, steroidal alkaloids have received special attention in anticancer activity recently. Substituted groups in chemical structure play markedly important roles in biological activities. Therefore, the effective way to obtain lead compounds quickly is structural modification, which is guided by structure–activity relationships (SARs). This review presents the SAR of steroidal alkaloids and anticancer, including pregnane alkaloids, cyclopregnane alkaloids, cholestane alkaloids, C-nor-D-homosteroidal alkaloids, and bis-steroidal pyrazine. A summary of SAR can powerfully help to design and synthesize more lead compounds.

Isothiocyanate Synthetic Analogs: Biological Activities, Structure-Activity Relationships and Synthetic Strategies

2014 ◽  
Vol 14 (12) ◽  
pp. 963-977 ◽  
Author(s):  
Andrea Milelli ◽  
Carmela Fimognari ◽  
Nicole Ticchi ◽  
Paolo Neviani ◽  
Anna Minarini ◽  
...  
Keyword(s):  
Biological Activities ◽  
Synthetic Analogs ◽  
Structure Activity Relationships ◽  
Structure Activity

scholarly journals Synthesis, Antiprotozoal Activity, and Cheminformatic Analysis of 2-Phenyl-2H-Indazole Derivatives

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2145
Author(s):  
Karen Rodríguez-Villar ◽  
Lilián Yépez-Mulia ◽  
Miguel Cortés-Gines ◽  
Jacobo David Aguilera-Perdomo ◽  
Edgar A. Quintana-Salazar ◽  
...  
Keyword(s):  
Phenyl Ring ◽  
Medicinal Chemistry ◽  
Structural Features ◽  
Pharmacological Properties ◽  
Antiprotozoal Activity ◽  
One Pot ◽  
Biological Assays ◽  
Structure Activity Relationships ◽  
Structure Activity ◽  
Synthetic Methodologies

Indazole is an important scaffold in medicinal chemistry. At present, the progress on synthetic methodologies has allowed the preparation of several new indazole derivatives with interesting pharmacological properties. Particularly, the antiprotozoal activity of indazole derivatives have been recently reported. Herein, a series of 22 indazole derivatives was synthesized and studied as antiprotozoals. The 2-phenyl-2H-indazole scaffold was accessed by a one-pot procedure, which includes a combination of ultrasound synthesis under neat conditions as well as Cadogan’s cyclization. Moreover, some compounds were derivatized to have an appropriate set to provide structure-activity relationships (SAR) information. Whereas the antiprotozoal activity of six of these compounds against E. histolytica, G. intestinalis, and T. vaginalis had been previously reported, the activity of the additional 16 compounds was evaluated against these same protozoa. The biological assays revealed structural features that favor the antiprotozoal activity against the three protozoans tested, e.g., electron withdrawing groups at the 2-phenyl ring. It is important to mention that the indazole derivatives possess strong antiprotozoal activity and are also characterized by a continuous SAR.

Design, synthesis and biological activities of pyrrole-3-carboxamide derivatives as EZH2 (enhancer of zeste homologue 2) inhibitors and anticancer agents

2020 ◽  
Vol 44 (6) ◽  
pp. 2247-2255
Author(s):  
Qifan Zhou ◽  
Lina Jia ◽  
Fangyu Du ◽  
Xiaoyu Dong ◽  
Wanyu Sun ◽  
...  
Keyword(s):  
Biological Activity ◽  
Anticancer Agents ◽  
Biological Activities ◽  
Activity Assay ◽  
Design Synthesis ◽  
Structure Activity Relationships ◽  
Structure Activity ◽  
Enhancer Of Zeste

A novel series of pyrrole-3-carboxamides targeting EZH2 have been designed and synthesized. The structure–activity relationships were summarized by combining with in vitro biological activity assay and docking results.

scholarly journals Structures, Activities and Drug-Likeness of Anti-Infective Xanthone Derivatives Isolated from the Marine Environment: A Review

Molecules ◽  
2019 ◽  
Vol 24 (2) ◽  
pp. 243 ◽  
Author(s):  
Daniela R. P. Loureiro ◽  
José X. Soares ◽  
Joana C. Costa ◽  
Álvaro F. Magalhães ◽  
Carlos M. G. Azevedo ◽  
...  
Keyword(s):  
Molecular Descriptors ◽  
Chemical Space ◽  
Biological Activities ◽  
Chemical Properties ◽  
Pharmacokinetic Parameters ◽  
Bioactive Substances ◽  
Xanthone Derivatives ◽  
Development Of Resistance ◽  
Marine Products ◽  
Infective Activity

Marine organisms represent almost half of total biodiversity and are a very important source of new bioactive substances. Within the varied biological activities found in marine products, their antimicrobial activity is one of the most relevant. Infectious diseases are responsible for high levels of morbidity and mortality and many antimicrobials lose their effectiveness with time due to the development of resistance. These facts justify the high importance of finding new, effective and safe anti-infective agents. Among the variety of biological activities of marine xanthone derivatives, one that must be highlighted is their anti-infective properties. In this work, a literature review of marine xanthones with anti-infective activity, namely antibacterial, antifungal, antiparasitic and antiviral, is presented. Their structures, biological activity, sources and the methods used for bioactivity evaluation are described. The xanthone derivatives are grouped in three sets: xanthones, hydroxanthones and glycosylated derivatives. Moreover, molecular descriptors, biophysico-chemical properties, and pharmacokinetic parameters were calculated, and the chemical space occupied by marine xanthone derivatives is recognized. The chemical space was compared with marketed drugs and framed accordingly to the drug-likeness concept in order to profile the pharmacokinetic of anti-infective marine xanthone derivatives.

scholarly journals A Comprehensive QSAR Study on Antileishmanial and Antitrypanosomal Cinnamate Ester Analogues

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4358 ◽  
Author(s):  
Freddy A. Bernal ◽  
Thomas J. Schmidt
Keyword(s):  
Biological Activities ◽  
Strong Dependence ◽  
Health Improvement ◽  
Underlying Structure ◽  
Parasitic Infections ◽  
Structure Activity Relationships ◽  
Structure Activity ◽  
Antitrypanosomal Activity ◽  
Validation Parameters ◽  
Test Sets

Parasitic infections like leishmaniasis and trypanosomiasis remain as a worldwide concern to public health. Improvement of the currently available drug discovery pipelines for those diseases is therefore mandatory. We have recently reported on the antileishmanial and antitrypanosomal activity of a set of cinnamate esters where we identified several compounds with interesting activity against L. donovani and T. brucei rhodesiense. For a better understanding of such compounds’ anti-infective activity, analyses of the underlying structure-activity relationships, especially from a quantitative point of view, would be a prerequisite for rational further development of such compounds. Thus, quantitative structure-activity relationships (QSAR) modeling for the mentioned set of compounds and their antileishmanial and antitrypanosomal activity was performed using a genetic algorithm as main variable selection tool and multiple linear regression as statistical analysis. Changes in the composition of the training/test sets were evaluated (two randomly selected and one by Kennard-Stone algorithm). The effect of the size of the models (number of descriptors) was also investigated. The quality of all resulting models was assessed by a variety of validation parameters. The models were ranked by newly introduced scoring functions accounting for the fulfillment of each of the validation criteria evaluated. The test sets were effectively within the applicability domain of the best models, which demonstrated high robustness. Detailed analysis of the molecular descriptors involved in those models revealed strong dependence of activity on the number and type of polar atoms, which affect the hydrophobic/hydrophilic properties causing a prominent influence on the investigated biological activities.

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