Jose L Medina-Franco

Universidad Nacional Autónoma de México | UNAM · Department of Pharmacy

The ability of epigenetic markers to affect genome function has enabled transformative changes in drug discovery, especially in cancer and other emerging therapeutic areas. Concordant with the introduction of the term ‘epi-informatics’, the size of the epigenetically relevant chemical space has grown substantially and so did the number of applicati...

In analogy with structure–activity relationships (SARs), which are at the core of medicinal chemistry, studying structure–inactivity relationships (SIRs) is essential to understanding and predicting biological activity. Current computational methods should predict or distinguish ‘activity’ and ‘inactivity’ with the same confidence because both conc...

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...

Metallodrug discovery has evolved in recent years, yielding several compounds in the clinic for therapeutic and medical imaging diagnostic applications. As reviewed here, several research groups in well-established medicinal inorganic chemistry groups are consistently generating high-quality SAR data representing an ideal starting point in the use...

COVID-19 has resulted in huge numbers of infections and deaths worldwide and brought the most severe disruptions to societies and economies since the Great Depression. Massive experimental and computational research effort to understand and characterize the disease and rapidly develop diagnostics, vaccines, and drugs has emerged in response to this...

Chemical libraries and compound data sets are among the main inputs to start the drug discovery process at universities, research institutes, and the pharmaceutical industry. The approach used in the design of compound libraries, the chemical information they possess, and the representation of structures, play a fundamental role in the development...

Understanding structure-activity landscapes is essential in drug discovery. Similarly, it has been shown that the presence of activity cliffs in compound data sets can have a substantial impact not only on the design progress but also can influence the predictive ability of machine learning models. With the continued expansion of the chemical space...

Since the number of drugs based on natural products (NPs) represents a large source of novel pharmacological entities, NPs have acquired significance in drug discovery. Peru is considered a megadiverse country with many endemic species of plants, terrestrial, and marine animals, and microorganisms. NPs databases have a major impact on drug discover...

Drug-induced liver injury (DILI) is the principal reason for failure in developing drug candidates. It is the most common reason to withdraw from the market after a drug has been approved for clinical use. In this context, data from animal models, liver function tests, and chemical properties could complement each other to understand DILI events be...

Entering the third decade of the 21st Century, artificial intelligence (AI) continues to offer significant advances in drug discovery. When used rationally beyond the hype, AI offers clear promise to advance further basic and applied research (Medina-Franco et al., 2021). At the same time, AI faces challenges to address at different levels. The pre...

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...

Protein-protein interaction (PPI) inhibitors have an increasing role in drug discovery. It is hypothesized that machine learning (ML) algorithms can classify or identify PPI inhibitors. This work describes the performance of different algorithms and molecular fingerprints used in chemoinformatics to develop a classification model to identify PPI in...

Pomegranate (PMG; Punica granatum L.) fruits possess a well-balanced nutrient/phytochemical composition, with proven adjuvant benefits in experimental cancer chemotherapy; however, such bioactivity could be affected by PMG’s phenogenotype (varietal). Here, the chemical and phytochemical (UPLC-DAD-MS2) composition, antioxidant capacity and anticance...

Background : Parkinson's disease is an attractive disease model to extend research towards a better understanding of the interrelationship between genes and the environment (exposome) therefore is an ideal model for a polypharmacological approach due to its clinical heterogeneity. Methods : In this paper, we present a series of polypharmacological...

Drug-induced liver injury (DILI) is the principal reason for failure in developing drug candidates. It is the most common reason to withdraw from the market after a drug has been approved for clinical use. Therefore, a current challenge is enhancing the accuracy of DILI events' predictive models. In this context, data from animal models, liver func...

Modification of the tubulin‐microtubule (Tub‐Mts) system has generated effective strategies for developing different treatments for cancer. A huge amount of clinical data about inhibitors of the tubulin‐microtubule system have supported and validated the studies on this pharmacological target. However, many tubulin‐microtubule inhibitors have been...

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...

In May 2022, JCAMD published a Special Issue in honor of Gerald (Gerry) Maggiora, whose scientific leadership over many decades advanced the fields of computational chemistry and chemoinformatics for drug discovery. Along the way, he has impacted many researchers in both academia and the pharmaceutical industry. In this Epilogue, we explain the ori...

Natural products (NPs) are a rich source of structurally novel molecules, and the chemical space they encompass is far from being fully explored. Over history, NPs have represented a significant source of bioactive molecules and have served as a source of inspiration for developing many drugs on the market. On the other hand, computer-aided drug de...

Natural products (NPs) are a rich source of structurally novel molecules, and the chemical space they encompass is far from being fully explored. Over history, NPs have represented a significant source of bioactive molecules and have served as a source of inspiration for developing many drugs on the market. On the other hand, computer-aided drug de...

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...

Protein-protein interaction (PPI) inhibitors have a continued and increasing role in drug discovery. It is hypothesized that machine learning (ML) algorithms are able to classify or identify PPI inhibitors. In this work, we describe the performance of different algorithms broadly used in chemoinformatics to develop a classification model able to id...

Informatics plays a fundamental role in many chemistry applications giving rise to the consolidation of well-established disciplines such as bioinformatics and chemoinformatics. It has also led to the maturation of subdisciplines such as food informatics, epi-informatics, and more recently, to the so-called natural products informatics. The extensi...

Protein-protein interaction (PPI) inhibitors have a continued and increasing role in drug discovery. It is hypothesized that machine learning (ML) algorithms are able to classify or identify PPI inhibitors. In this work, we describe the performance of different algorithms broadly used in chemoinformatics to develop a classification model able to id...

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...

The concept of chemical space is a cornerstone in chemoinformatics, and it has broad conceptual and practical applicability in many areas of chemistry, including drug design and discovery. One of the most considerable impacts is in the study of structure–property relationships where the property can be a biological activity or any other characteris...

Inhibitors of epigenetic writers such as DNA methyltransferases (DNMTs) are attractive compounds for epigenetic drug and probe discovery. To advance epigenetic probes and drug discovery, chemical companies are developing focused libraries for epigenetic targets. Based on a knowledge-based approach, herein we report the identification of two quinazo...

Phenolic acids represent a large collection of phytochemical molecules present in the plant kingdom; they have an important role as epigenetic regulators, particularly as inhibitors of DNA methylation. In the present study, 14 methyl benzoate and cinnamate analogs were synthesized (11‐24). Their cytotoxic activity on hepatocellular carcinoma cells...

Inhibitors of epigenetic writers such as DNA methyltransferases (DNMTs) are attractive compounds for epigenetic drug and probe discovery. There are many small molecules tested as inhibitors of DNMTs but, overall, they do not have potent enzymatic inhibition. Chemical companies are developing focused libraries for epigenetic targets to advance probe...

The primary goal of scientific publishing is to disseminate results and, in general, advance science. However, the enormous pressure of publishing in different settings, particularly academia, influences scientific publishing to the point of becoming a survival mechanism under the notion of “publish or perish.". Such conception distorts the main go...

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Transcription factors associated with quorum sensing in P. aeruginosa are promising targets for discovering new adjuvants against infection with this pathogen. Regulation of these transcription factors offers the possibility of controlling multiple virulence factors related to them as biofilm development, proteases, hydrogen cyanide, among others....

Natural products have a significant role in drug discovery. Their unique chemical structures have led to compounds in clinical use to treat different diseases. Also, natural products are significant sources of inspiration or starting points to develop new therapeutic agents. There are also unique natural products such as peptides and macrocycles th...

The importance of epigenetic drug and probe discovery is on the rise. This is not only paramount to identify and develop therapeutic treatments associated with epigenetic processes but also to understand the underlying epigenetic mechanisms involved in biological processes. To this end, chemical vendors have been developing synthetic compound libra...

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,...

Inhibitors of DNA methyltransferases (DNMTs) are attractive compounds for epigenetic drug discovery. They are also chemical tools to understand the biochemistry of epigenetic processes. Herein, we report five distinct inhibitors of DNMT1 characterized in enzymatic inhibition assays that did not show activity with DNMT3B. It was concluded that the d...

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...

Taking decisions is one of the most challenging duties that Human beings must do. We are making choices all the time, from simple and everyday life decisions to more complicated ones that require careful thinking, planning, and Human intelligence of various kinds, including analytical and emotional. Typically, trivial decisions have limited or shor...

The primary goal of scientific publishing is to disseminate results and, in general, advance science. However, the enormous pressure of publishing in different settings, particularly academia, influences scientific publishing to the point of becoming a survival mechanism under the 'publish or perish" paradigm. Such a paradigm distorts the main goal...

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...

The importance of epigenetic drug and probe discovery is on the rise. This is not only paramount to identify and develop therapeutic treatments associated with epigenetic processes but also to understand the underlying epigenetic mechanisms involved in biological processes. To this end, chemical vendors have been developing synthetic compound libra...

The importance of epigenetic drug and probe discovery is on the rise. This is not only paramount to identify and develop therapeutic treatments associated with epigenetic processes but also to understand the underlying epigenetic mechanisms involved in biological processes. To this end, chemical vendors have been developing synthetic compound libra...

The search for novel therapeutic compounds remains an overwhelming task owing to the time-consuming and expensive nature of the drug development process and low success rates. Traditional methodologies that rely on the one drug-one target paradigm have proven insufficient for the treatment of multifactorial diseases, leading to a shift to multitarg...

Nowadays, infectious diseases caused by drug-resistant bacteria have become especially important. Linezolid is an antibacterial drug active against clinically important Gram positive strains; however, resistance showed by these bacteria has been reported. Nanotechnology has improved a broad area of science, such as medicine, developing new drug del...

Epigenetic drug discovery is a promising avenue to find therapeutic agents for treating several diseases and developing novel chemical probes for research. In order to identify hit and lead compounds, the chemical space has been explored and screened, generating valuable bioactivity information that can be used for multiple purposes such as predict...

We report the major conclusions of the online open-access workshop "Computational Applications in Secondary Metabolite Discovery (CAiSMD)" that took place from 08 to 10 March 2021. Invited speakers from academia and industry and about 200 registered participants from five continents (Africa, Asia, Europe, South America, and North America) took part...

Isothiocyanates (ITCs) have a significant impact on food and natural product chemistry. Several dietary components and food chemicals contain the isothiocyanate moiety. In addition, many ITCs interact with macromolecules of biological relevance, making these compounds relevant for potential therapeutic applications and disease prevention. However,...

Despite the contributions of CADD in different stages of the drug discovery pipelines and technological advances, there are challenges that need to be addressed. Table 1 outlines the grand challenges that face drug discovery using in silico methods and AI and are further commented on in this manuscript. The list of topics is not exhaustive; the sel...

Transcription factors associated with quorum sensing in P. aeruginosa are promising targets for developing new adjuvants against infection by this pathogen. Regulation of these transcription factors offers the possibility of controlling multiple virulence factors related to them, as the development of biofilm, proteases, hydrogen cyanide, and other...

Transcription factors associated with quorum sensing in P. aeruginosa are promising targets for developing new adjuvants against infection by this pathogen. Regulation of these transcription factors offers the possibility of controlling multiple virulence factors related to them, as the development of biofilm, proteases, hydrogen cyanide, and other...

The current hype associated with machine learning and artificial intelligence often confuses scientists and students and may lead to uncritical or inappropriate applications of computational approaches. Even the field of computer-aided drug design (CADD) is not an exception. The situation is ambivalent. On one hand, more scientists are becoming awa...

In this study, we evaluated 3444 Latin American natural products using cheminformatic tools. We also characterized 196 compounds for the first time from the flora of El Salvador that were compared with the databases of secondary metabolites from Brazil, Mexico, and Panama, and 42 969 compounds (natural, semi-synthetic, synthetic) from different reg...

In this study, we evaluated 3444 Latin American natural products using cheminformatic tools. We also characterized 196 compounds for the first time from the flora of El Salvador that were compared with the databases of secondary metabolites from Brazil, Mexico, and Panama, and 42 969 compounds (natural, semi-synthetic, synthetic) from different reg...

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...

Aim: Evaluate the in vitro effect of coumarin and 15 monosubstituted derivatives on the inhibition of human platelet aggregation induced by various pro-aggregatory agonists, particularly by epinephrine. Background: The emergence of residual platelet reactivity during the use of conventional antiplatelet agents (acetylsalicylic acid and clopidogr...

Inhibiting the tubulin-microtubules (Tub-Mts) system is a classic and rational approach for treating different types of cancers. A large amount of data on inhibitors in the clinic supports Tub-Mts as a validated target. However, most of the inhibitors reported thus far have been developed around common chemical scaffolds covering a narrow region of...

Natural products continue to be a significant source of active compounds [...].

As chemical information evolves, impacting many chemistry areas, effective ways to disseminate results by the scientific community are also changing. Thus, publication schemes adapt to meet the needs of researchers across disciplines to share high-quality data, information, and knowledge. Since 2015, the F1000Research Chemical Information Science (...

According to the CDC´s 2019 Antibiotic Resistance Threats Report, infections caused by multidrug-resistant P. aeruginosa compromised about 32,600 hospitalized patients and 2,700 deaths in the United States during 2017. Therefore, new agents against Pseudomonas aeruginosa are an urgent necessity. Transcription factors (TF) associated with quorum sen...

The acidic and basic functional groups in a molecule strongly influence its physicochemical properties, affinity for a macromolecule, pharmacokinetics, and toxicity. For instance, basicity has been correlated with molecular promiscuity, hERG blockade, and phospholipidosis. Nonetheless, no systematic characterization of the acid/base profile of epig...

Epigenetic targets are of significant importance in drug discovery research, as demonstrated by the eight approved epigenetic drugs for treatment of cancer and the increasing availability of chemogenomic data related to epigenetics. This data represents many structure-activity relationships that have not been exploited thus far to develop predictiv...

The identification of protein targets of small molecules is essential for drug discovery. With the increasing amount of chemogenomic data in the public domain, multiple ligand-based models for target prediction have emerged. However, these models are generally biased by the number of known ligands for different targets, which involves an under-repr...

Informatics is growing across disciplines, impacting several areas of chemistry, biology, and biomedical sciences. Besides the well-established bioinformatics discipline, other informatics-based interdisciplinary fields have been evolving over time, such as chemoinformatics and biomedical informatics. Other related research areas such as pharmacoin...

Natural products are an invaluable source of molecules with a large variety of biological activities. Interest in natural products in drug discovery is documented in an increasing number of publications of bioactive secondary metabolites. Among those, medicinal plants are one of the most studied for this endeavor. An ever thriving area of opportuni...