Andrés Fernando González Barrios

• PhD
• Professor (Associate) at Los Andes University (Colombia)

Therapeutic strategies for Alzheimer’s disease (AD) often involve inhibiting acetylcholinesterase (AChE), underscoring the need for novel inhibitors with high selectivity and minimal side effects. A detailed analysis of the protein-ligand pharmacophore dynamics can facilitate this. In this study, we developed and employed dyphAI, an innovative appr...

Flavor is the main factor driving consumers acceptance of food products. However, tracking the biochemistry of flavor is a formidable challenge due to the complexity of food composition. Current methodologies for linking individual molecules to flavor in foods and beverages are expensive and time-consuming. Predictive models based on machine learni...

Surfactants are molecules derived primarily from petroleum that can reduce the surface tension at interfaces. Their slow degradation is a characteristic that could cause environmental issues. This and other factors contribute to the allure of biosurfactants today. Progress has been made in this area of research, which aims to satisfy the need for e...

In this study a Machine Learning model was employed to predict the lipid profile from supercritical fluid extraction (SFE) of microalgae Galdieria sp. USBA-GBX-832 under different temperature (40, 50, 60°C), pressure (150, 250 bar), and ethanol flow (0.6, 0.9 mL min⁻¹) conditions. Six machine learning regression models were trained using 33 indepen...

Fungi are diverse organisms with various characteristics and functions. Some play a role in recycling essential elements, such as nitrogen and carbon, while others are utilized in the food and drink production industry. Some others are known to cause diseases in various organisms, including humans. Fungal pathogens cause superficial, subcutaneous,...

Dengue (DENV) and Zika (ZIKV) virus continue to pose significant challenges globally due to their widespread prevalence and severe health implications. Given the absence of effective vaccines and specific therapeutics, targeting the highly conserved NS5 RNA-dependent RNA polymerase (RdRp) domain has emerged as a promising strategy. However, limited...

Bacterial structures formed from the outer membrane and the periplasm components carry biomolecules to expel cellular material and interact with other cells. These outer membrane vesicles (OMVs) can encapsulate bioactive content, which gives OMVs a high potential as alternative drug delivery vehicles or as a platform for novel vaccine development....

Flavor is the main factor driving consumers acceptance of food products. However, tracking the biochemistry of flavor is a formidable challenge due to the complexity of food composition. Current methodologies for linking individual molecules to flavor in foods and beverages are expensive and time-consuming. Predictive models based on machine learni...

Dengue (DENV) and Zika (ZIKV) virus continue to pose significant challenges globally due to their widespread prevalence and severe health implications. Given the absence of effective vaccines and specific therapeutics, targeting of the highly conserved NS5 RNA-dependent RNA polymerase (RdRp) domain has emerged as a promising strategy. However, limi...

Flavor is the main factor driving consumers acceptance of food products. However, tracking the biochemistry of flavor is a formidable challenge due to the complexity of food composition. Current methodologies for linking individual molecules to flavor in foods and beverages are expensive and time-consuming. Predictive models based on machine learni...

Enzyme–substrate interactions play a fundamental role in elucidating synthesis pathways and synthetic biology, as they allow for the understanding of important aspects of a reaction. Establishing the interaction experimentally is a slow and costly process, which is why this problem has been addressed using computational methods such as molecular dy...

Naringenin is the central flavonoid in the biosynthesis of several bioactive compounds and presents a growing demand for its nutraceutical properties. Naringenin extraction from plants is non-viable due to low yields, and microbial platforms could represent a controlled and sustained alternative to produce it using several metabolic engineering too...

El aceite de la coraza de marañón (ACM) es un subproducto de alto interés en la industria química por sus aplicaciones en el diseño de materiales poliméricos, surfactantes y componentes bioactivos. Sin embargo, dentro de la cadena productiva del marañón en el Departamento del Vichada este subproducto ha sido poco explorado. Para recuperar el ACM se...

Over the past decades, Colombia has suffered complex social problems related to illicit crops, including forced displacement, violence, and environmental damage, among other consequences for vulnerable populations. Considerable effort has been made in the regulation of illicit crops, predominantly Cannabis sativa, leading to advances such as the le...

Wound healing is a complex process involving blood cells, extracellular matrix, and parenchymal cells. Research on biomimetics in amphibian skin has identified the CW49 peptide from Odorrana grahami, which has been demonstrated to promote wound regeneration. Additionally, lavender essential oil exhibits anti-inflammatory and antibacterial activitie...

Computational modeling and simulation of biological systems have become valuable tools for understanding and predicting cellular performance and phenotype generation. This work aimed to construct, model, and dynamically simulate the virulence factor pyoverdine (PVD) biosynthesis in Pseudomonas aeruginosa through a systemic approach, considering tha...

Parkinson’s disease (PD) is the second most common neurodegenerative disorder after Alzheimer’s disease. Therefore, development of novel technologies and strategies to treat PD is a global health priority. Current treatments include administration of Levodopa, monoamine oxidase inhibitors, catechol-O-methyltransferase inhibitors, and anticholinergi...

The molecule (2S)-naringenin is a scaffold molecule with several nutraceutical properties. Currently, (2S)-naringenin is obtained through chemical synthesis and plant isolation. However, these methods have several drawbacks. Thus, heterologous biosynthesis has emerged as a viable alternative to its production. Recently, (2S)-naringenin production s...

The global market of chocolate has increased worldwide during the last decade and is expected to reach a value of USD 200 billion by 2028. Chocolate is obtained from different varieties of Theobroma cacao L, a plant domesticated more than 4000 years ago in the Amazon rainforest. However, chocolate production is a complex process requiring extensive...

For many years, Colombia was one of the countries with the largest illegal cultivation of cannabis around the world. Currently, it is going through a period of transition with a new government law that recently allows the cultivation, transformation, and commercialization of such plant species. In this sense, the identification of strategies for th...

Antifolates such as methotrexate (MTX) have been largely known as anticancer agents because of their role in blocking nucleic acid synthesis and cell proliferation. Their mechanism of action lies in their ability to inhibit enzymes involved in the folic acid cycle, especially human dihydrofolate reductase (hDHFR). However, most of them have a class...

Wound healing in adult mammals results in scar formation, which prevents recovering the full functionality of the original skin. This area of dermatology is constantly evolving and especially focuses on aging and the design of recovery treatments for skin burns. Because it has been reported that Lavandula angustifolia essential oil and the CW49 pep...

Skin burns are injuries of different degrees of complexity (first to third) caused by physical and/or chemical trauma. There is a necessity to improve the rapid retrieval of superficial wounds (first grade) to enhance epithelization, avoiding dehydration, infections, and scar formation. This work proposes an oil in water (O/W) emulsion based on 1%...

Community acquired infections caused by Meticillin-resistant Staphylococcus aureus (MRSA) have become a growing concern due to its impact on the world public health. This microorganism is a commonly spreading pathogen associated predominantly with skin infections and connected to other more severe conditions (septic shock, and generalized infection...

Producto de la revisión detallada de la formación en ingeniería y el perfil profesional del programa en Ingeniería Química del Departamento de Ingeniería Química y de Alimentos de la Universidad de Los Andes, se adelantó un proceso de reforma curricular, dando lugar a los llamados Cursos Proyecto, que fueron ejecutados e integrados al plan de estud...

As the world enters its second year of the pandemic caused by SARS-CoV-2, intense efforts have been directed to develop an effective diagnosis, prevention, and treatment strategies. One promising drug target to design COVID-19 treatments is the SARS-CoV-2 M pro . To date, a comparative understanding of M pro dynamic stereoelectronic interactions wi...

The impact of cocoa lipid content on chocolate quality has been extensively described. Nevertheless, few studies have elucidated the cocoa lipid composition and their bioactive properties, focusing only on specific lipids. In the present study the lipidome of fine-flavor cocoa fermentation was analyzed using LC-MS-QTOF and a Machine Learning model...

Enzymatic hydrolysis of proteins is a breakdown process of peptide bond in proteins, releasing some peptides with potential biological functions. Previous studies on enzymatic hydrolysis of whey proteins have not identified the complete peptide profiles after hydrolysis. In this study, we reconstructed a profile of peptides from whey hydrolysates w...

Cocoa fermentation plays a crucial role in producing flavor and bioactive compounds of high demand for food and nutraceutical industries. Such fermentations are frequently described as a succession of three main groups of microorganisms (i.e., yeast, lactic acid, and acetic acid bacteria), each producing a relevant metabolite (i.e., ethanol, lactic...

Due to metabolic engineering advances, it is possible to produce a large number of bio-based chemical compounds. However, the downstream processing is challenging the development at an industrial scale. Selecting the proper recovery and separation method is critical in developing a cost-effective and competitive process. This study is focused on an...

Recent developments in High Throughput Sequencing (HTS) technologies and bioinformatics, including improved read lengths and genome assemblers allow the reconstruction of complex genomes with unprecedented quality and contiguity. Sugarcane has one of the most complicated genomes among grassess with a haploid length of 1Gbp and a ploidies between 8...

Fragment-based drug design (FBDD) and pharmacophore modeling have proven to be efficient tools to discover novel drugs. However, these approaches may become limited if the collection of fragments is highly repetitive, poorly diverse, or excessively simple. In this article, combining pharmacophore modeling and a non-classical type of fragmentation (...

Cyclin-Dependent Kinase 2 (CDK2) and Vascular-Endothelial Growth Factor Receptor 2 (VEGFR2) are promising targets for the design of novel inhibitors in anticancer therapeutics. In a recent work, our group designed a set of potential dual inhibitors predicted to occupy an allosteric back pocket near the active site of both enzymes, but their dynamic...

The global demand for fine-flavour cocoa has increased worldwide during the last years. Fine-flavour cocoa offers exceptional quality and unique fruity and floral flavour attributes of high demand by the world's elite chocolatiers. Several studies have highlighted the relevance of cocoa fermentation to produce such attributes. Nevertheless, little...

Selecting appropriate metabolic engineering targets to build efficient cell factories maximizing the bioconversion of industrial by-products to valuable compounds taking into account time restrictions is a significant challenge in industrial biotechnology. Microbial metabolism engineering following a rational design has been widely studied. However...

Chemical modifications of proteins during food processing can lead to new functionalities and applications of products. Enzymatic hydrolysis, with Alcalase and Flavourzyme, of whole whey was carried out in different conditions, including pH (5.5, 7.0 and 8.5), temperature (42, 50, and 58°C), enzyme‐substrate ratio (E/S) (1, 2, and 3%), and duration...

The development of a culture medium is an essential step in any bioprocess involving microorganisms for the bioconversion of by‐products to valuable chemicals, making industries like the biofuel industry more competitive. Optimization of the bioconversion process to minimize cost while maximizing yield underscores the importance of using computatio...

Background Glycerol has become an interesting carbon source for industrial processes as consequence of the biodiesel business growth since it has shown promising results in terms of biomass/substrate yields. Selecting the appropriate metabolic targets to build efficient cell factories and maximize the desired chemical production in as little time a...

The oil and gas industry generates large amounts of oil-derived effluents such as Heavy Crude Oil (HCO) in water (W) emulsions, which pose a significant remediation and recovery challenge due to their high stability and the presence of environmentally concerning compounds. Nanomaterials emerge as a suitable alternative for the recovery of such effl...

Clostridium (Ruminiclostridium) thermocellum is recognized for its ability to ferment cellulosic biomass directly, but it cannot naturally grow on xylose. Recently, C. thermocellum (KJC335) was engineered to utilize xylose through expressing a heterologous xylose catabolizing pathway. Here, we compared KJC335′s transcriptomic responses to xylose ve...

Xanthomonas phaseoli pv. manihotis (Xpm) is the causal agent of cassava bacterial blight, the most important bacterial disease in this crop. There is a paucity of knowledge about the metabolism of Xanthomonas and its relevance in the pathogenic process, with the exception of the elucidation of the xanthan biosynthesis route. Here we report the reco...

Malassezia yeasts are lipid dependent and part of the human and animal skin microbiome. However, they are also associated with a variety of dermatological conditions and even cause systemic infections. How these yeasts can live as commensals on the skin and switch to a pathogenic stage has long been a matter of debate. Lipids are important cellular...

Microbial cell factories have been used for the production of valuable chemical compounds using a classical metabolic engineering approach, but this requires much time and cost, and labor‐intensive processes to make cell factories industrially competitive. Systems metabolic engineering is an upgraded version, which understands the cell as a complex...

Cyclin-Dependent Kinase 2 (CDK2) and Vascular Endothelial Growth Factor Receptor (VEGFR2) have largely been considered as attractive targets for developing anticancer agents. However, there is no dual inhibitor commercially available in the market that interacts simultaneously with the allosteric back pocket of these enzymes. We applied a combined...

The green revolution has resulted in many new opportunities and challenges for the chemical industry. Specifically, there is an increasing tendency for using natural ingredients in product formulation, and, as a result, an increase in the complexity of product formulation. A way to address this is through a multiscale strategy that allows for deepe...

The opportunistic pathogen Malassezia pachydermatis causes bloodstream infections in preterm infants or individuals with immunodeficiency disorders and has been associated with a broad spectrum of diseases in animals such as seborrheic dermatitis, external otitis and fungemia. The current approaches to treat these infections are failing as a conseq...

Dye-sensitized solar cells (DSSCs) have been highlighted as the promising alternative to generate clean energy based on low pay-back time materials. These devices have been designed to mimic solar energy conversion processes from photosynthetic organisms (the most efficient energy transduction phenomenon observed in nature) with the aid of low-cost...

Dye-sensitized solar cells (DSSCs) have been highlighted as the promising alternative to generate clean energy based on low pay-back time materials. These devices have been designed to mimic solar energy conversion processes from photosynthetic organisms (the most efficient energy transduction phenomenon observed in nature) with the aid of low-cost...

Outer membrane protein A (OmpA) has been extensively studied in Gram-negative bacteria due to its relevance in the adhesion of pathogens to host cells and its surfactant capabilities. It consists of a hydrophobic β-barrel domain and a hydrophilic periplasmic domain, that confers OmpA an amphiphilic structure. This study aims to elucidate the capaci...

Malassezia pachydermatis is part of the skin microbiota and can act as an opportunistic pathogen causing external otitis and seborrheic dermatitis in dogs and cats, as well as dermatologic diseases and fungemia in humans[1,2]. Dermatological conditions caused by M. pachydermatis are chronic, recurrent, and show variations in their susceptibilit...

The Escherichia coli’s membrane protein OmpA has been identified as a potential biosurfactant due to their amphiphilic nature, and their capacity to stabilize emulsions of dodecane in water. In this study, the influence of surfactant type, concentration, preservation time and droplet size on the crystallization of n-dodecane and water, in oil-in-wa...

Malassezia pachydermatis hace parte de la microbiota de la piel pero puede actuar como un patógeno oportunista causando otitis externa y dermatitis seborreica en perros y gatos[1], así como afecciones dérmicas y fungemias en humanos[2]. Además, se ha demostrado que las infecciones dermatológicas de M. pachydermatis son crónicas, recurrentes y muest...

The ligand efficiency (LE) indexes have long been used as decision-making criteria in drug discovery and development. However, in the context of fragment-based drug design (FBDD), these metrics often exhibit a strong emphasis toward the selection of highly efficient “core” fragments for potential optimization, which are not usually considered as pa...

Oils and fats are important raw materials in food products, animal feed, cosmetics, and pharmaceuticals among others. The market today is dominated by oils derive, d from African palm, soybean, oilseed and animal fats. Colombia’s Amazon region has endemic palms such as Euterpe precatoria (açai), Oenocarpus bataua (patawa), and Mauritia flexuosa (bu...

One of the main challenges in the food industry is to design strategies for the successful incorporation of natural sources of bioactive compounds. Recently, yogurts and other fermented dairy beverages have been proposed as ideal carriers of such bioactive compounds such as fatty acids and antioxidants that could improve consumers' health. However,...

Poultry products are one of the major transmission media of Salmonella enteritidis to humans. A promising alternative to reduce the load of Salmonella in poultry are bacteriophages. Elsewhere, a mixture of six bacteriophages has been used successfully, but large‐scale production would be necessary to supply potential poultry market and costs analys...

The development of new technologies for environmental reparation has allowed the application of inexpensive alternatives such as bioremediation, with a high potential to treat ecosystems contaminated with hydrocarbons. Microalgae-bacteria consortia have been identified as an efficient alternative for the detoxification of organic and inorganic cont...

Background Extensive experimentation has been conducted to increment 1,3-propanediol (PDO) production using Clostridium butyricum cultures in glycerol, but computational predictions are limited. Previously, we reconstructed the genome-scale metabolic (GSM) model iCbu641, the first such model of a PDO-producing Clostridium strain, which was validate...

Adjustment of the kinetic models used as constraints. (PDF)

Front, side and top views of Figs 9 and 10. (PDF)

Random profiles used in the global sensitivity analyses. (PDF)

Comparison of DFBA predictions using different orthogonal polynomials. (PDF)

Development of the population balance model. (PDF)

Biosurfactants are biomolecules capable of altering interfacial tension of emulsions. Since they are produced by different microorganisms and are biodegradable their use in water-in-oil separation is being studied. In this work, Escherichia coli outer membrane protein, OmpN, was immobilized on magnetic nanoparticles (MNPs) to explore their applicat...

The increase in atmospheric CO2 due to anthropogenic activities is generating climate change, which has resulted in a subsequent rise in global temperatures with severe environmental impacts. Biological mitigation has been considered as an alternative for environmental remediation and reduction of greenhouse gases in the atmosphere. In fact, the us...

Canonical discriminant functions analysis of metabolomic data (A) grouping by time (B) grouping by growth condition and time

Response surface of growth rates predicted by FBA in function of CO2 and acetate fluxes [mmol/gDW h]

Canonical discriminant analysis of metabolomic data (A) heterotrophic growth condition (0% CO2) (B) mixotrophic growth condition (10% CO2)

New comprehensive genome-scale network reconstruction for C. reinhardtii, which consisted of 3726 reactions and 2436 metabolites

New comprehensive genome-scale network reconstruction for C. reinhardtii

Effects on different metabolic pathways, such as glycerolipid synthesis, amino acid synthesis, glycolysis, carbohydrate catabolism, and carbon fixation, among others

Transport phenomena is proposed as the second paradigm as a consequence of the inadequacy of the unit operations field for solving process and product engineering problems. The appearance of Bird’s transport phenomena textbook put transport phenomena as an engineering science along with thermodynamics for chemical engineers. Even though this field...