Yovani Marrero-Ponce

Universidad San Francisco de Quito (USFQ) · Department of Human Medicine

In the last two decades many reports have addressed the application of artificial intelligence (AI) in the search and design of antimicrobial peptides (AMPs). AI has been represented by machine learning (ML) algorithms that use sequence-based features for the discovery of new peptidic scaffolds with promising biological activity. From AI perspectiv...

Disease vector insects rely on chemosensors to locate hosts, find mates and choose where to lay their eggs. Currently, the most efficient method of preventing and controlling the outbreak of insect-borne diseases is the use of Insect Repellents (IRs). However, current IRs have significant drawbacks and do not meet the necessary conditions, such as...

With the advancement of combinatorial chemistry and big data, drug repositioning has boomed. In this sense, machine learning and artificial intelligence techniques offer a priori information to identify the most promising candidates. In this study, we combine QSAR and docking methodologies to identify compounds with potential inhibitory activity of...

Peptide-based drugs are promising anticancer candidates due to their biocompatibility and low toxicity. In particular, tumor-homing peptides (THPs) have the ability to bind specifically to cancer cell receptors and tumor vasculature. Despite their potential to develop antitumor drugs, there are few available prediction tools to assist the discovery...

A review on the effectiveness, safety, cost and cost-effectiveness of visual laser ablation of the prostate (VLAP), prostatic urethral lift (PUL), transurethral water vapour ablation (TUWA), transurethral resection of the prostate (TURP), transurethral needle ablation (TUNA), transurethral microwave thermotherapy (TUMT), holmium-YAG laser enucleati...

Antimicrobial peptides (AMPs) have appeared as promising compounds to treat a wide range of diseases. Their clinical potentialities reside in the wide range of mechanisms they can use for both killing microbes and modulating immune responses. However, the hugeness of the AMPs’ chemical space (AMPCS), represented by more than 1065 unique sequences o...

Peptide-based drugs are promising anticancer candidates due to their biocompatibility, and low toxicity. Particularly, tumor homing peptides (THPs) have the ability to bind specifically to can-cer cells receptors and tumor vasculature. Despite their potential to develop antitumor drugs, there are few available prediction tools to assist the discove...

High-throughput methods in science have created a trend to generate massive amount of data that challenge our ability to mine and search through massive information spaces. Thus more efficient and effective solutions for data analysis and optimization are required continuously. The best solutions for many problems-solving approaches in science coul...

Antimicrobial peptides (AMPs) are small bioactive chemicals that have appeared as promising compounds to treat a wide range of diseases. The effectiveness of AMPs resides in the wide range of mechanisms they can use for both killing microbes and modulating immune responses. However, the AMPs’ chemical space (AMPCS) is huge, it is estimated that the...

Antimicrobial peptides (AMPs) are small bioactive chemicals that have appeared as promising compounds to treat a wide range of diseases. The effectiveness of AMPs resides in the wide range of mechanisms they can use for both killing microbes and modulating immune responses. However, the AMPs’ chemical space (AMPCS) is huge, it is estimated that the...

The selenoenzyme glutathione peroxidase (GPx) like activity of stable organoselenium compounds has been evaluated through the initial rate (ν0) of the reduction reaction of H2O2, Cum-OOH, and t-BuOOH. A Quantitative Structure–Activity Relationships (QSAR) analysis based on different machine learning techniques was performed by employing atom-weighe...

Enquiries about the content of the report should be emailed to hta@health.gov.au. The technical information in this document is used by the Medical Services Advisory Committee (MSAC) to inform its deliberations. MSAC is an independent committee which has been established to provide advice to the Minister for Health on the strength of evidence avail...

During this work, the viability of encapsulated replicators systems as a function of the vesicle size is revisited. Now, instead of considering in detail the diffusion process, the existence of a well-mixed solution inside the vesicle was assumed. Our results corroborated previous numerical estimations about the existence of a minimal size for vesi...

In this report, we introduce a set of aggregation operators (AOs) to calculate global and local (group and atom type) molecular descriptors (MDs) as a generalization of the classical approach of molecular encoding using the sum of the atomic (or fragment) contributions. These AOs are implemented in a new and free software denominated MD-LOVIs (http...

Abstract The increasing interest in bioactive peptides with therapeutic potentials has been reflected in a large variety of biological databases published over the last years. However, the knowledge discovery process from these heterogeneous data sources is a nontrivial task, becoming the essence of our research endeavor. Therefore, we devise a uni...

Drug-induced liver injury (DILI) is a key safety issue in the drug discovery pipeline and a regulatory concern. Thus, many in silico tools have been proposed to improve the hepatotoxicity prediction of organic-type chemicals. Here, classifiers for the prediction of DILI were developed by using QuBiLS-MAS 0−2.5D molecular descriptors and shallow mac...

SI 2, 3, 4 and 5

Table of Contents SI1.I. Graph (discrete) Derivative Theory as support of GDIs. 3 SI1.1. Graph (discrete) Derivative Theory as support of GDIs. 4 SI1.1.1. High Order Derivative. 6 SI1.1.2. Mixed Derivative. 6 SI1.2. Hypermatrix and Graph Derivatives over n-elements. 7 SI1.3. Events. 10 SI1.3.1. Terminal Paths. 11 SI1.3.2. Vertex Path Incidence. 12...

Advances to the distributed, multi-core and fully cross-platform QuBiLS-MIDAS soft-ware v2.0 (http://tomocomd.com/qubils-midas) are reported in this article since the v1.0 release. The most recent features added to the QuBiLS-MIDAS software v2.0 are related (a) to the calculation of atomic weightings from indices based on the vertex-degree invarian...

This material is available free of charge via the Internet…and the description is given: SI1_i: It is a folder with the optimized 3D structure of all datasets used in this work. SI1_ii: It is a excel word containing the smile of each molecules and the corresponding DILI class of each compounds in all the datasets. SI2_i: It’s a folder with an .arff...

Background: Medicinal phytochemistry involving UPLC-DAD in an exhaustive analysis involving quantification of eight commercially important phytochemicals viz. syringin, cordifolioside A, magnoflorine, tinocordiside, palmatine, 20β-hydroxyecdysone, L-tetrahydropalmatine and berberine has been done in 143 accessions from eight states and the union t...

This report introduces the MuLiMs-MCoMPAs software (acronym for Multi-Linear Maps based on N-Metric and Contact Matrices of 3D Protein and Amino-acid weightings), designed to compute tensor-based 3D protein structural descriptors by applying two- and three-linear algebraic forms. Moreover, these descriptors contemplate generalizing components such...

A novel spherical truncation method, based on fuzzy membership functions, is introduced to truncate interatomic (or interaminoacid) relations according to smoothing values computed from fuzzy membership degrees. In this method, the molecules are circumscribed into a sphere, so that the geometric centers of the molecules are the centers of the spher...

Docking based selectiity panel

In this report, a new type of tridimensional (3D) biomacro-molecular descriptors for proteins are proposed. These descriptors make use of multi-linear algebra concepts based on the application of 3-linear forms (i.e., Canonical Trilinear (Tr), Trilinear Cubic (TrC), Trilinear-Quadratic-Bilinear (TrQB) and so on) as a specific case of the N-linear a...

SMII-Projects_and_data

Background: Recently, some authors have defined new molecular descriptors (MDs) based on the use of the Graph Discrete Derivative, known as Graph Derivative Indices (GDI). This new approach about discrete derivatives over various elements from a graph takes as outset the formation of subgraphs. Previously, these definitions were extended into the...

Quantitative structure-activity relationships (QSAR) are introduced to predict acute oral toxicity (AOT), by using the QuBiLS-MAS framework for the molecular encoding. Three training sets were employed to build the models: EPA training set (5931 compounds), EPA-full training set (7413 compounds) and Zhu training set (10152 compounds). Additionally,...

MOTIVATION: Bioactive peptides have gained great attention in the academy and pharmaceutical industry since they play an important role in human health. However, the increasing number of bioactive peptide databases is causing the problem of data redundancy and duplicated efforts. Even worse is the fact that the available data is non-standardized an...

A problem-based learning experience integrating mathematical concepts of linear and abstract algebra for undergraduate chemistry students is presented. The pedagogical framework was focused on the conceptual understanding of the vector space, graph theory and matrix algebra as a tool to obtain chemical information. The students were capable to solv...

Supplementary Data: In SI1 is the summary of events used for the molecular fragmentation. SI2 shows the Table with Norms, Means and Statistical Invariants as Generalizations of the Linear Combination of LOVIs as Global (or Local) MDs Operator, as well as Classical algorithms which generalize the first three groups. The SI3 contains the best MLR equ...

Several topological (2D) and geometric (3D) molecular descriptors (MDs) are calculated from local vertex/edge invariants (LOVIs/LOEIs) by performing an aggregation process. To this end, norm-, mean- and statistic-based (non-fuzzy) operators are used, under the assumption that LOVIs/LOEIs are independent (orthogonal) values of one another. These ope...

A different perspective to compute global weighted definitions of molecular descriptors from the contributions of each atom (LOVIs) or covalent bond (LOEIs) within a molecule is presented, using the generalized ordered weighted averaging - weighted averaging (GOWAWA) aggregation operator. This operator is rather different from the other norm-, mean...

Aim: Metronidazole is the most widely used drug in trichomoniasis therapy. However, the emergence of metronidazole-resistant Trichomonas vaginalis isolates calls for the search for new drugs to counter the pathogenicity of these parasites. Results: Classification models for predicting the antitrichomonas activity of molecules were built. These m...

Atomic Weighted Vectors (AWVs) are vectors that contain the codified information of molecular structures, which can apply to a set of Aggregation Operators (AOs) to calculate total and local molecular descriptors (MDs). This article presents an exploratory study of a new tool useful for drug discovery using different datasets, such as DRAGON and Su...

After the identification of the anti-inflammatory properties of the VA5-13l (2-benzyl-1-methyl-5-nitroindazolinone) in previous investigations, some analogous compounds of them were designed, synthesized and evaluated in two anti-inflammatory methods: LPS-enhanced leukocyte migration assay in zebrafish and 12-O-tetradecanoylphorbol-13-acetate (TPA)...

In a recent article was described in silico repositioning, design, synthesis, biological evaluation and structure-activity relationship (SAR) of an original class of anti-inflammatory agents based on a polyaromatic pharmacophore structurally related to bisacodyl (BSL) drug used in therapeutic as laxative.

Quantitative Structure - Activity Relationship (QSAR) modeling has been widely used in medicinal chemistry and computational toxicology for many years. Today, as the amount of data on chemicals is increasing dramatically, QSAR methods have become pivotal for the purpose of handling the data, identifying a decision, and gathering useful information...

This was a poster presented at the AICHE Annual Meeting held on Minneapolis, MN

Several descriptors from atom weighted vectors are used in the prediction of aquatic toxicity of set of organic compounds of 392 benzene derivatives to the protozoo ciliate Tetrahymena pyriformis (log(IGC50)(-1)). These descriptors are calculated using the MD-LOVIs software and various Aggregation Operators are examined with the aim comparing their...

Background: There are a great number of tools that can be used in QSAR/QSPR studies; they are implemented in several programs that are reviewed in this report. The usefulness of new tools can be proved through comparison, with previously published approaches. In order to perform the comparison the most usual is the use of several benchmark dataset...

A comprehensive and largest (to the best of our knowledge) database of 791 essential oil components (EOCs) with corresponding gas chromatographic retention properties has been built. With this data set, Quantitative structure–retention relationship (QSRR) models for the prediction of the Kováts retention indices (RIs) on the non-polar DB-5 stationa...

A novel mathematical procedure to codify chiral features of organic molecules in the QuBiLS-MIDAS framework is introduced. This procedure constitutes a generalization to that commonly used to date, where the values 1 and -1 (correction factor) are employed to weight the molecular vectors when each atom is labelled as R (rectus) or S (sinister) acco...

A novel algebraic-based method for the geometric characterization of proteins and peptides.

Background In previous reports, Marrero-Ponce et al. proposed algebraic formalisms for characterizing topological (2D) and chiral (2.5D) molecular features through atom- and bond-based ToMoCoMD-CARDD (acronym for Topological Molecular Computational Design-Computer Aided Rational Drug Design) molecular descriptors. These MDs codify molecular informa...

Herein is described in silico repositioning, design, synthesis, biological evaluation and structure-activity relationship (SAR) of an original class of anti-inflammatory agents based on a polyaromatic pharmacophore structurally related to bisacodyl (BSL) drug used in therapeutic as laxative. We describe the potential of TOMOCOMD-CARDD methods to fi...

Graph Derivative Indices (GDIs) have been recently defined over N-atoms (N = 2, 3 and 4) simultaneously, which are based on the concept of derivatives in discrete mathematics (Finite Difference), metaphorical to the derivative concept in classical mathematical analysis. These molecular descriptors (MDs) codify topo-chemical and topo-structural info...

Helminths infections remain a major problem in medical and public health. In this report, atom-based 2D bilinear indices, a TOMOCOMD-CARDD (QuBiLs-MAS module) molecular descriptor family and linear discriminant analysis (LDA) were used to find models that differentiate among anthelmintic and non-anthelmintic compounds. Two classification models obt...

The NS2B-NS3 protease is essential for the Dengue Virus (DENV) replication process. This complex constitutes a target for efficient antiviral discovery because a drug could inhibit the viral polyprotein processing. Furthermore, since the protease is highly conserved between the four Dengue virus serotypes, it is probable that a drug would be equall...

Introducción: la leishmaniasis es una enfermedad provocada por protozoos del género Leishmania, cuyas repercusiones pueden ser fatales o provocar discapacidad. En el presente trabajo se identifican nuevos compuestos con potencial actividad antileishmaniásica empleando estudios in silico. Objetivo: confeccionar una nueva base de datos de compuestos...

Epigenetic drug discovery is a promising research field with growing interest in the scientific community, as evidenced by the number of publications and the large amount of structure-epigenetic activity information currently available in the public domain. Computational methods are valuable tools to analyse and understand the activity of large com...

N-Glycosylation is a common post-translational modification that plays an important role in the proper folding and function of many proteins. This modification is largely dependent on the presence of a sequence motif called a “sequon” defined as Asn-Xxx-Ser/Thr. However, evidence has shown that the presence of such a “sequon” is insufficient to det...

The search for new selective pharmacological agents with no significant side-effects is an increasing requirement for the development of new drugs to be used in the treatment of acute and chronic pain. In the present study, a new series of compounds (VAM 1, 6, 10, 11, 12, 2-4) has been screening in QSAR-LDA mathematic models and pharmacologically e...

Molecular descriptors from atom weighted vectors (MD-AWV) are used in the prediction of aquatic toxicity of a large group of organic compounds of 392 benzene derivatives to the protozoo ciliate Tetrahymena pyriformis (log (IGC50) −1). These descriptors are calculated using the MD-LOVIs software and various Aggregation Operators are examined with th...

Identificación de compuestos líderes con potencial actividad antileishmaniásica: una contribución a la farmacéutica médica. ABSTRACT Introduction: leishmaniasis is a disease caused by protozoan parasites of the genus Leishmania; its repercussions can be fatal and cause disability. In the present work, some new compounds with potential antileishmani...

The QSAR studies defined in the literature are based on uni-modal approaches and do not consider datasets with different chemical information. Thus, this research has as objective to apply and analyze the behavior of multi-modal approaches when QSAR studies are carried out. To this end, a compound dataset with hepatotoxicity activity was employed a...

Novel N-tuple topological/geometric cutoffs to consider specific inter-atomic relations in the QuBiLS-MIDAS framework are introduced in this manuscript. These molecular cutoffs permit the taking into account of relations between more than two atoms by using (dis-)similarity multi-metrics and the concepts related with topological and Euclidean-geome...

The control of electromechanical responses within bonding regions is essential to face frontier challenges in nanotechnologies, such as molecular electronics and biotechnology. Here, we present Iβ-nanocellulose as a potentially new orthotropic 2D piezoelectric crystal. The predicted in-layer piezoelectricity is originated on a sui-generis hydrogen...