Fernanda I. Saldivar-Gonzalez

National Autonomous University of Mexico | UNAM · Department of Pharmacy

Virtual compound libraries are increasingly being used in computer-assisted drug discovery applications and have led to numerous successful cases. This paper aims to examine the fundamental concepts of library design and describe how to enumerate virtual libraries using open source tools. To exemplify the enumeration of chemical libraries, we empha...

Natural products (NPs) are primarily recognized as privileged structures to interact with protein drug targets. Their unique characteristics and structural diversity continue to marvel scientists for developing NP-inspired medicines, even though the pharmaceutical industry has largely given up. High-performance computer hardware, extensive storage,...

El desarrollo e investigación de fármacos es un proceso complejo que a menudo se percibe más como un arte que como una ciencia. Las muchas incógnitas de las enfermedades humanas, su complejidad, y el gran tamaño del espacio químico para encontrar fármacos potenciales, hacen que la toma de decisiones en Química Farmacéutica sea excepcionalmente exig...

Virtual small molecule libraries are valuable resources for identifying bioactive compounds in virtual screening campaigns and improving the quality of libraries in terms of physicochemical properties, complexity, and structural diversity. In this context, the computational-aided design of libraries focused against antidiabetic targets can provide...

Food is more than just fuel. On one hand, it is a way to show love and care, and it holds stories from the people around us, our ancestors, and their traditions. On the other hand, food also influences how we feel and perceive ourselves. The more we understand the ways foods can change how our bodies work, the more we can understand how our diets a...

Alzheimer’s disease (AD), a prevalent neurodegenerative disorder, presents significant challenges in drug development due to its multifactorial nature and complex pathophysiology. The AlzyFinder Platform, introduced in this study, addresses these challenges by providing a comprehensive, free web-based tool for parallel ligand-based virtual screenin...

Designing and developing inhibitors against the epigenetic target DNA methyltransferase (DNMT) is an attractive strategy in epigenetic drug discovery. DNMT1 is one of the epigenetic enzymes with significant clinical relevance. Structure-based de novo design is a drug discovery strategy that was used in combination with similarity searching to ident...

Searching, retrieving, and analyzing chemical information are among the main tasks faced by students and professionals in chemistry-related scientific disciplines. Currently, freely available modules developed in programming languages, such as Python, allow efficient data management and facilitate the obtaining of information and knowledge from the...

Designing and developing inhibitors against the epigenetic target DNA methyltransferase (DNMT) is an attractive strategy in epigenetic drug discovery. DNMT1 is one of the epigenetic enzymes with significant clinical relevance. Structure-based de novo design is a drug discovery strategy used in combination with similarity searching to identify a nov...

The chapter discusses recent advances on computer-aided drug discovery with particular emphasis on the concept and broad applications of chemical space and chemical or molecular multiverses. We also briefly describe progress on selected concepts, methodologies, resources, and applications that are part of multidisciplinary efforts in drug discovery...

Searching, retrieving, and analyzing chemical information is one of the main tasks faced by students and professionals in chemistry-related scientific disciplines. Currently, freely available modules developed in programming languages, such as Python, allow efficient data management and facilitate obtaining information and knowledge from the data....

The structure-activity relationships data available in public databases of inhibitors of DNA methyltransferases (DNMTs), families of epigenetic targets, plus the structural information of DNMT1, enables the development of a robust structure-based drug design strategy to study, at the molecular level, the activity of DNMTs inhibitors. In this study,...

Cuando se habla de Química, lo más común es imaginar a alguien dentro de un laboratorio, portando goggles, vistiendo una bata y trabajando con matraces (el llamado “laboratorio húmedo” o wet lab). Sin embargo, también existen hombres y mujeres que están detrás de una computadora haciendo experimentos, pero con algoritmos (el llamado “laboratorio se...

Science and art have been connected for centuries. With the development of new computational methods, new scientific disciplines have emerged, such as computational chemistry, and related fields, such as cheminformatics. Chemoinformatics is grounded on the chemical space concept: a multi-descriptor space in which chemical structures are described....

Science and art have been connected for centuries. With the development of new computational methods, new scientific disciplines have emerged, such as computational chemistry, and related fields, such as chemoinformatics that use informatic methods to solve chemical problems focusing on small molecules. Chemoinformatics is grounded on the chemical...

We report the main conclusions of the first Chemoinformatics and Artificial Intelligence Colloquium, Mexico City, June 15–17, 2022. Fifteen lectures were presented during a virtual public event with speakers from industry, academia, and non-for-profit organizations. Twelve hundred and ninety students and academics from more than 60 countries. Durin...

The manuscript discusses recent advances on computer-aided drug discovery (CADD) with focus on data-dependent drug discovery. Herein, we do not intend to review the many CADD methodologies comprehensively. Instead, the review discusses progress on selected concepts, methodologies, resources, and applications that are part of multidisciplinary effor...

We report the main conclusions of the first Chemoinformatics and Artificial Intelligence Colloquium, Mexico City, June 15-17, 2022. Fifteen lectures were presented during a virtual public event with speakers from industry, academia, and non-for-profit organizations. Twelve hundred and ninety students and academics from more than 60 countries. Durin...

Technological advances and practical applications of the chemical space concept in drug discovery, natural product research, and other research areas have attracted the scientific community's attention. The large- and ultra-large chemical spaces are associated with the significant increase in the number of compounds that can potentially be made and...

We report the main conclusions of the first Chemoinformatics and Artificial Intelligence Colloquium, Mexico City (virtual), June 15-17, 2022. Fifteen lectures were presented during a virtual and public event with speakers from industry, academia, and non-for-profit organizations. 1,290 participants, including students and academics from more than 6...

Introduction: Chemical space is a powerful, general, and practical conceptual framework in drug discovery and other areas in chemistry that addresses the diversity of molecules and it has various applications. Moreover, chemical space is a cornerstone of chemoinformatics as a scientific discipline. In response to the increase in the set of chemica...

Technological advances and practical applications of the chemical space concept in drug discovery, natural product research, and other research areas have attracted the scientific community´s attention. The large- and ultra-large chemical spaces are associated not only with the significant increase in the number of compounds that can potentially be...

Chemical space is a powerful, general, and practical conceptual framework in drug discovery and other areas in chemistry that addresses the diversity of molecules and it has various applications. Moreover, chemical space is a cornerstone of chemoinformatics as a scientific discipline. In response to the increase in the set of chemical compounds in...

Acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV) continues to be a public health problem. In 2020, 680,000 people died from HIV-related causes, and 1.5 million people were infected. Antiretrovirals are a way to control HIV infection but not to cure AIDS. As such, effective treatment must be developed to con...

The acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV) continues to be a public health problem. In 2020, 680,000 people died from HIV-related causes, and 1.5 million people were infected. Antiretrovirals are only a way to control HIV infection but not to cure AIDS. As such, effective treatment must be develop...

Al nuevo uso de medicamentos ya existentes, y que ya han sido probados en estudios clínicos, se le conoce como reposicionamiento de fármacos. Es una estrategia muy útil para proponer y probar fármacos, particularmente en crisis y emergencias sanitarias donde existen pocas o nulas opciones terapéuticas. El reposicionamiento de fármacos ofrece innume...

Natural products have a significant role in drug discovery. Natural products have distinctive chemical structures that have contributed to identifying and developing drugs for different therapeutic areas. Moreover, natural products are significant sources of inspiration or starting points to develop new therapeutic agents. Natural products such as...

Small molecule libraries for virtual screening are becoming a well-established tool for the identification of new hit compounds. As for experimental assays, the library quality, defined in terms of structural complexity and diversity, is crucial to increase the chance of a successful outcome in the screening campaign. In this context, Diversity-Ori...

The chemical space of naturally occurring compounds is vast and diverse. Other than biologics, naturally occurring small molecules include a large variety of compounds covering natural products from different sources such as plant, marine, and fungi, to name a few, and several food chemicals. The systematic exploration of the chemical space of natu...

Volume 1 of Chemoinformatics of Natural Products lays down the fundamental concepts of chemical informatics and is exclusively dedicated to the investigation of natural products (NPs) or secondary metabolites (SMs), the main source of lead compounds for drug discovery. Several experts in the field, working in different continents and from diverse b...

Small molecules have always been of interest in medicinal chemistry because of their ability to exert significant effects on the functions of macromolecules that comprise living systems. Chemical diversity and complexity are examples of properties to guide the design and selection of new small molecules. These properties may have significant implic...

Small Molecule Drug Discovery: Methods, Molecules and Applications presents the methods used to identify bioactive small molecules, synthetic strategies and techniques to produce novel chemical entities and small molecule libraries, chemoinformatics to characterize and enumerate chemical libraries, and screening methods, including biophysical techn...

Lactams are a class of compounds important for drug design, due to their great variety of potential therapeutic applications, spanning cancer, diabetes, and infectious diseases. So far, the biological profile and chemical diversity of lactams have not been characterized in a systematic and detailed manner. In this work, we report the chemoinformati...

NuBBEDB is the first library of natural products of Brazilian biodiversity. It includes a large variety of classes of compounds and structural types of secondary metabolites of plants, fungi, insects, marine organisms and bacteria. So far the chemical diversity and complexity of NuBBEDB has not been characterized in a systematic and detailed manner...

Compound databases of natural products have a major impact on drug discovery projects and other areas of research. The number of databases in the public domain with compounds with natural origins is increasing. Several countries, Brazil, France, Panama and, recently, Vietnam, have initiatives in place to construct and maintain compound databases th...

Natural products (NPs) have been shown to be an extraordinary source of bioactive compounds and three-dimensionally complex frameworks that can be useful to produce high-value molecular collections able to address “undruggable” and difficult therapeutic targets. Bicyclic acetals are particularly relevant for these purposes, given their key role in...

Herein is presented a tutorial overview on selected chemoinformatics methods useful for assembling, curating/preparing a chemical database, and assessing its diversity and chemical space. Methods for evaluating the structure–activity relationships (SAR) and polypharmacology are also included. Usage of open source tools is emphasized. Step-by-step K...

The chemical space of naturally occurring compounds is vast and diverse. Other than biologics, naturally occurring small molecules include a large variety of compounds covering natural products from different sources such as plant, marine, and fungi, to name a few, and several food chemicals. The systematic exploration of the chemical space of natu...

Compound databases of natural products have a major impact on drug discovery projects and other areas of research. The number of databases in the public domain with compounds from natural origin is increasing. Several countries have initiatives in place to construct and maintain compound databases that are representative of their diversity. Example...

Naturally occurring small molecules include a large variety of natural products from different sources that have confirmed activity against epigenetic targets. In this work we review chemoinformatic, molecular modeling, and other computational approaches that have been used to uncover natural products as inhibitors of DNA methyltransferases, a majo...

Naturally occurring small molecules include a large variety of natural products from different sources that have confirmed activity against epigenetic targets. In this work we review chemoinformatic, molecular modeling and other computational approaches that have been used to uncover natural products as inhibitors of DNA metiltransferases, a major...

The aim of the present study was to demonstrate that ivermectin preferentially inhibited cancer stem‑like cells (CSC) in breast cancer cells and downregulated the expression of 'stemness' genes. Computational searching of DrugBank, a database of approved drugs, was performed using the principles of two‑dimensional similarity searching; the chemical...

In light of the high relevance of polypharmacology, multi-target screening is a major trend in drug discovery. As such, the increasing amount of available structure–activity data requires the application of chemoinformatic approaches to mine structure–multiple activity relationships. To this end, activity landscape methods, initially developed to e...

El descubrimiento de fármacos es un proceso complejo y costoso en el cual convergen diversas áreas del conocimiento. En años recientes métodos computacionales se han integrado a este esfuerzo multidisciplinario y su enseñanza en cursos de Química Farmacéutica es fundamental. En un proyecto determinado, la aplicación de estrategias de cómputo depend...