Rafael E. O. Rocha

ORCID: 0000-0002-4314-1220
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About
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Research Areas
  • Computational Drug Discovery Methods
  • Crime, Illicit Activities, and Governance
  • Microbial Metabolic Engineering and Bioproduction
  • Protein Structure and Dynamics
  • Scientific Computing and Data Management
  • Youth, Drugs, and Violence
  • Enzyme Structure and Function
  • Biofuel production and bioconversion
  • Trypanosoma species research and implications
  • Machine Learning in Materials Science
  • SARS-CoV-2 and COVID-19 Research
  • Cholinesterase and Neurodegenerative Diseases
  • Bioactive Compounds and Antitumor Agents
  • Mosquito-borne diseases and control
  • Malaria Research and Control
  • Suicide and Self-Harm Studies
  • RNA and protein synthesis mechanisms
  • Meta-analysis and systematic reviews
  • Crime Patterns and Interventions
  • Enzyme Production and Characterization
  • Research on Leishmaniasis Studies
  • Virology and Viral Diseases
  • Toxoplasma gondii Research Studies
  • Urban and sociocultural dynamics
  • Machine Learning in Bioinformatics

Universidade Federal de Minas Gerais
2018-2024

Inserm
2024

Régulations Naturelle et Artificielle
2024

Institut Européen de Chimie et Biologie
2024

Université de Bordeaux
2024

Univates
2024

Federal University of São João del-Rei
2023

Centro Universitário de Sete Lagoas
2022

University of Salzburg
2021

Protein-peptide interactions play a fundamental role in wide variety of biological processes, such as cell signaling, regulatory networks, immune responses, and enzyme inhibition. Peptides are characterized by low toxicity small interface areas; therefore, they good targets for therapeutic strategies, rational drug planning protein Approximately 10% the ethical pharmaceutical market is protein/peptide-based. Furthermore, it estimated that 40% mediated peptides. Despite fast increase volume...

10.1186/s12859-020-03881-z article EN cc-by BMC Bioinformatics 2021-01-02

The worldwide COVID-19 pandemic caused by the coronavirus SARS-CoV-2 urgently demands novel direct antiviral treatments. main protease (Mpro) and papain-like (PLpro) are attractive drug targets among coronaviruses due to their essential role in processing polyproteins translated from viral RNA. In this study, we virtually screened 688 naphthoquinoidal compounds derivatives against Mpro of SARS-CoV-2. Twenty-four were selected evaluated biochemical assays using a fluorogenic substrate....

10.1021/acs.jcim.2c00693 article EN Journal of Chemical Information and Modeling 2022-08-12

Around three billion people are at risk of infection by the dengue virus (DENV) and potentially other flaviviruses. Worldwide outbreaks DENV, Zika (ZIKV), yellow fever (YFV), lack antiviral drugs, limitations on vaccine usage emphasize need for novel research. Here, we propose a consensus virtual screening approach to discover potential protease inhibitors (NS3pro) against different flavivirus. We employed an in silico combination hologram quantitative structure–activity relationship (HQSAR)...

10.1021/acs.jcim.3c01505 article EN Journal of Chemical Information and Modeling 2024-01-09

The main-protease (Mpro) catalyzes a crucial step for the SARS-CoV-2 life cycle. recent presents main protease (MCoV2pro) with 12 mutations compared to SARS-CoV (MCoV1pro). Recent studies point out that these subtle differences lead mobility variances at active site loops functional implications. We use metadynamics simulations and sort of computational analysis probe dynamic, pharmacophoric catalytic environment between monomers both enzymes. So, we verify how much intrinsic distinctions...

10.1080/07391102.2021.1924271 article EN Journal of Biomolecular Structure and Dynamics 2021-05-10

β-Glucosidases are enzymes with high importance for many industrial processes, catalyzing the last and limiting step of conversion lignocellulosic material into fermentable sugars biofuel production. However, β-glucosidases inhibited by concentrations product (glucose), which limits production on an scale. For this reason, structural mechanisms tolerance to inhibition have been target several studies. In study, we performed in silico experiments, such as molecular dynamics (MD) simulations,...

10.3390/molecules24183215 article EN cc-by Molecules 2019-09-04

Abstract The phylum Apicomplexa comprises eukaryotic parasites that cause fatal diseases affecting millions of people and animals worldwide. Their mitochondrial genomes have been significantly reduced, leaving only three protein-coding genes highly fragmented mitoribosomal rRNAs, raising challenging questions about mitoribosome composition, assembly structure. Our study reveals how Toxoplasma gondii assembles over 40 mt-rRNA fragments using exclusively nuclear-encoded proteins...

10.1038/s41467-024-55033-z article EN cc-by Nature Communications 2024-12-17

Bioinformatics research depends on high-quality databases to provide accurate results. In silico experiments, correctly performed, may prospect novel discoveries and elucidates pathways for biological experiments through data analysis in large scale. However, most have presented mistakes, such as incorrectly classified or incomplete information. Also, sometimes, mining algorithms cannot treat these errors, leading serious problems the analysis. Manual curation of extracted from literature is...

10.48550/arxiv.1707.05813 preprint EN other-oa arXiv (Cornell University) 2017-01-01

β-glucosidases (EC 3.2.1.21) have been described as essential to second-generation biofuel production. They act in the last step of lignocellulosic saccharification, cleaving β − 1,4 glycosidic bonds cellobiose produce two molecules glucose. However, strongly inhibited by glucose, causing an increment concentration. Also, is inhibitor other enzymes used this process, such exoglucanases and endoglucanases. Hence, engineering thermostable glucose-tolerant has targeted many studies. In study,...

10.1080/07391102.2020.1734484 article EN Journal of Biomolecular Structure and Dynamics 2020-02-28

The NS2B-NS3 protease (NS2B-NS3pro) is regarded as an interesting molecular target for drug design, discovery, and development because of its essential role in the Zika virus (ZIKV) cycle. Although no NS2B-NS3pro inhibitors have reached clinical trials, employment drug-like scaffolds can facilitate screening process new compounds. In this study, we performed a combination ligand-based structure-based silico methods targeting two known non-peptide small-molecule with micromolar inhibitory...

10.3390/ph16091319 article EN cc-by Pharmaceuticals 2023-09-19

Abstract Background Protein engineering has many applications for industry, such as the development of new drugs, vaccines, treatment therapies, food, and biofuel production. A common way to engineer a protein is perform mutations in functionally essential residues optimize their function. However, discovery beneficial proteins complex task, with time-consuming high cost experimental validation. Hence, computational approaches have been used propose insights experiments narrowing search...

10.1186/s12859-020-03575-6 article EN cc-by BMC Bioinformatics 2020-07-01

Abstract Β-glucosidases are key enzymes used in second-generation biofuel production. They act the last step of lignocellulose saccharification, converting cellobiose glucose. However, most β-glucosidases inhibited by high glucose concentrations, which turns it a limiting for industrial Thus, have been targeted several studies aiming to understand mechanism tolerance, pH and thermal resistance constructing more efficient enzymes. In this paper, we present database β-glucosidase structures,...

10.1186/s12860-020-00293-y article EN cc-by BMC Molecular and Cell Biology 2020-07-01

Abstract Trypanosomatids are protozoan parasites responsible for leishmaniasis, Chagas disease and sleeping sickness. The design of new antitrypanosomatid drugs with trypanosomicidal leishmanicidal activities is an effective perspective. thiazolidinone ring important scaffold several biological disorders. Herein, 4‐oxothiazolidine‐5‐acetic acids ( 1 a‐1 w ) have been synthesized from respective thiosemicarbazone maleic anhydride. Some these were toxic trypomastigotes without affecting...

10.1002/slct.201902561 article EN ChemistrySelect 2019-12-02

The worldwide COVID-19 pandemic caused by the coronavirus SARS-CoV-2 urgently demands novel direct antiviral treatments. main protease (Mpro) and papain-like (PLpro) are attractive drug targets among coronaviruses due to their essential role in processing polyproteins translated from viral RNA. In present work, we virtually screened 688 naphthoquinoidal compounds derivatives against Mpro of SARS-CoV-2. Twenty-four were selected evaluated biochemical assays using a fluorogenic substrate....

10.1101/2022.01.05.475095 preprint EN bioRxiv (Cold Spring Harbor Laboratory) 2022-01-05

Galantamine (Gnt) is a natural alkaloid inhibitor of acetylcholinesterase and presently one the most used drugs in treatment against Alzheimer's disease during both initial intermediate stages. Among several Gnt derivatives, sanguinine (Sng) lycoramine (Lyc) attract attention because way their subtle chemical differences from lead to drastic opposite distinctions inhibitory effects. However, date, there no solved structure for these derivatives. In present study, we applied computational...

10.1080/07391102.2018.1470036 article EN Journal of Biomolecular Structure and Dynamics 2018-04-26

Este artigo analisa experiências juvenis diante de esforços governança criminal nas periferias Maceió, em Alagoas, e Belo Horizonte, Minas Gerais. Partimos jovens não envolvidos para evidenciar que estar fora do crime é mundo , uma vez suas vidas são atravessadas por regimes morais justiça grupos criminais nos territórios onde vivem circulam. Argumentamos a instabilidade das dinâmicas Maceió Horizonte faz da guerra forma relação central atravessa relações parentesco, amorosas, vizinhança,...

10.4322/dilemas.v15nesp4.46076 article PT cc-by Dilemas - Revista de Estudos de Conflito e Controle Social 2022-01-01

Abstract β‐glucosidases play a pivotal role in second‐generation biofuel (2G‐biofuel) production. For this application, thermostable enzymes are essential due to the denaturing conditions on bioreactors. Random amino acid substitutions have originated new β‐glucosidases, but without clear understanding of their molecular mechanisms. Here, we probe by different dynamics simulation approaches with distinct force fields and submitting results various computational analyses, bases...

10.1002/prot.26424 article EN Proteins Structure Function and Bioinformatics 2022-09-17

Chagas disease is a neglected tropical parasitic caused by the protozoan Trypanosoma cruzi. Worldwide, an estimated 8 million people are infected with T. cruzi, causing more than 10,000 deaths per year. Currently, only two drugs, nifurtimox and benznidazole (BNZ), approved for its treatment. However, both ineffective during chronic phase, show toxicity, produce serious side effects. This work aimed to obtain evaluate novel 2-nitroimidazole-N-acylhydrazone derivatives analogous BNZ. The...

10.1002/ardp.202400059 article EN Archiv der Pharmazie 2024-04-16

O comportamento suicida inclui desde ideação à morte por suicídio. É um fenômeno multicausal sendo responsável 800.000 mortes ao ano no mundo. Fatores psicopatológicos relacionados a traços de impulsividade, sentimentos desesperança e adversidades na infância podem contribuir para explicação deste comportamento. objetivo do presente estudo foi comparar uma amostra indivíduos com tentativas suicídio (TS) (IS) residentes região Vale Taquari/RS controles mesma região, levando em consideração o...

10.55905/cuadv16n6-091 article PT cc-by-nc Cuadernos de Educación y Desarrollo 2024-06-14

This article examines the relationships of violent rivalry among youth gangs in city Belo Horizonte, Brazil. Based on extensive fieldwork multiple gangs, authors discuss how gang rivalries are structured and renewed over decades. Through this in-depth examination role determining structure membership these characteristics observed can contribute to existing international literature gangs.

10.24201/es.2020v38n113.1719 article EN cc-by-nc-nd Estudios Sociológicos de El Colegio de México 2020-04-21

Phytases [myo-inositol(1,2,3,4,5,6) hexakisphosphate phosphohydrolases] are phytate-specific phosphatases not present in monogastric animals. Nevertheless, they an essential supplement to feeding such animals and for human special diets. It is crucial, hence, the biotechnological use of phytases with intrinsic stability activity at acid pHs from gastric environments. Here we Metadynamics (METADY) simulations probe conformational space

10.1080/07391102.2023.2223685 article EN Journal of Biomolecular Structure and Dynamics 2023-06-16

O artigo visa examinar os discursos e elementos simbólicos mobilizados por atores inseridos no “mundo do crime” para justificar ou condenar assassinatos na Zona Leste de Belo Horizonte, área periférica da cidade. A pesquisa, baseada análise inquéritos policiais entrevistas, se concentrou em investigar o modo como esses fazem uso uma gramática moral forma justificação legitimidade considerar injustos, que configura ofensa a ser reparada meio retaliações violentas.

10.17648/dilemas.v13n3.23152 article PT cc-by Dilemas - Revista de Estudos de Conflito e Controle Social 2020-09-13

Ligand-based screening of large molecular databases can help reduce costs with experiments by filtering and ranking promising compounds in an initial stage the drug developing process.However, some ligand-based methods be ineffective when presented a high-dimensional number attributes extracted from extensive dataset compounds.Herein, we propose drugmining algorithm that used to screen ligands repurpose known drugs, any for target.The Milk-Way combines mathematical regression select without...

10.31300/tdb.13.2020.1-20 article EN Trends in Developmental Biology 2020-09-22

This article analyzes youth experiences in the face of criminal governance efforts peripheries Alagoas state capital Maceió and Minas Gerais Belo Horizonte. We consider young people who are not involved crime to demonstrate that being “outside crime” is same as outside “world crime,” view fact trajectories their lives affected by moral legal regimes territories where they live through which pass. argue instable dynamics Horizonte transform gang war into a form central relationship intersects...

10.4322/dilemas.v15esp4.52525 article EN cc-by Dilemas - Revista de Estudos de Conflito e Controle Social 2022-01-01
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