scholarly journals ANCESTRAL RECONSTRUCTION OF A β-LACTAMASE AND COMPARISON WITH ITS EXTANT PROTEINS

2021 ◽  
pp. 155-170
Author(s):  
Gonzalo Fernández Balaguer ◽  
Carmen del Águila ◽  
Carolina Hurtado Marcos ◽  
Rubén Agudo Torres
Keyword(s):  
High Capacity ◽  
Hydrolytic Activity ◽  
Point Of View ◽  
New Drugs ◽  
Ancestral Reconstruction ◽  
Ancestral Sequences ◽  
Starting Point ◽  
Evolution Of Proteins ◽  
Ancestral Protein

The β-lactamases are proteins of bacterial origin that are characterized by hydrolyzing antibiotics β-lactams, conferring microbial resistance against them. They are a heterogeneous family of proteins very relevant from a health point of view due to the ease they present to acquire resistance to new drugs due to their high capacity for evolution. The in vitro evolution of these proteins has served not only to develop their characterization and improve their knowledge, but as a new line of research that allows to predictively identify residues involved in the acquisition of antibiotic resistance. At the same time, the method of ancestral protein reconstruction has been revealed as a novel and useful tool to understand the evolution of β-lactamases and understand some of their characteristics such as their promiscuity. In this work, a study of ancestral β-lactamases reconstructed from the phylogeny of existing class A β-lactamases has been carried out. Of the four ancestral proteins studied, one has been obtained that is functional and has compared its hydrolytic activity with that of four of its current counterparts against eight β-lactam drugs. This ancestral protein has been shown to have a more generalistic antibiotic activity than any of the current proteins studied. In addition, the active ancestral protein showed more resistance to one of the drugs used than the rest of β-lactamases existing. Finally these results have been discussed and from them it is argued why reconstructed ancestral sequences can be a very attractive starting point when it comes to direct evolution of proteins for obtaining proteins of biotechnological interest.

Enzyme Promiscuous Activity: How to Define it and its Evolutionary Aspects

2020 ◽  
Vol 27 (5) ◽  
pp. 400-410
Author(s):  
Valentina De Luca ◽  
Luigi Mandrich
Keyword(s):  
Gene Evolution ◽  
Sequence Divergence ◽  
High Specificity ◽  
Industrial Applications ◽  
Point Of View ◽  
Enzyme Promiscuity ◽  
Primary Activity ◽  
Starting Point ◽  
Main Activity

: Enzymes are among the most studied biological molecules because better understanding enzymes structure and activity will shed more light on their biological processes and regulation; from a biotechnological point of view there are many examples of enzymes used with the aim to obtain new products and/or to make industrial processes less invasive towards the environment. Enzymes are known for their high specificity in the recognition of a substrate but considering the particular features of an increasing number of enzymes this is not completely true, in fact, many enzymes are active on different substrates: this ability is called enzyme promiscuity. Usually, promiscuous activities have significantly lower kinetic parameters than to that of primary activity, but they have a crucial role in gene evolution. It is accepted that gene duplication followed by sequence divergence is considered a key evolutionary mechanism to generate new enzyme functions. In this way, promiscuous activities are the starting point to increase a secondary activity in the main activity and then get a new enzyme. The primary activity can be lost or reduced to a promiscuous activity. In this review we describe the differences between substrate and enzyme promiscuity, and its rule in gene evolution. From a practical point of view the knowledge of promiscuity can facilitate the in vitro progress of proteins engineering, both for biomedical and industrial applications. In particular, we report cases regarding esterases, phosphotriesterases and cytochrome P450.

Design of Inhibitors for Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) Enzyme of Leishmania mexicana

2020 ◽  
Vol 16 (6) ◽  
pp. 784-795
Author(s):  
Krisnna M.A. Alves ◽  
Fábio José Bonfim Cardoso ◽  
Kathia M. Honorio ◽  
Fábio A. de Molfetta
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Site ◽  
Point Of View ◽  
New Drugs ◽  
Leishmania Mexicana ◽  
Receptor Complexes ◽  
Starting Point ◽  
Dynamics Simulations ◽  
Selection Of

Background:: Leishmaniosis is a neglected tropical disease and glyceraldehyde 3- phosphate dehydrogenase (GAPDH) is a key enzyme in the design of new drugs to fight this disease. Objective:: The present study aimed to evaluate potential inhibitors of GAPDH enzyme found in Leishmania mexicana (L. mexicana). Methods: A search for novel antileishmanial molecules was carried out based on similarities from the pharmacophoric point of view related to the binding site of the crystallographic enzyme using the ZINCPharmer server. The molecules selected in this screening were subjected to molecular docking and molecular dynamics simulations. Results:: Consensual analysis of the docking energy values was performed, resulting in the selection of ten compounds. These ligand-receptor complexes were visually inspected in order to analyze the main interactions and subjected to toxicophoric evaluation, culminating in the selection of three compounds, which were subsequently submitted to molecular dynamics simulations. The docking results showed that the selected compounds interacted with GAPDH from L. mexicana, especially by hydrogen bonds with Cys166, Arg249, His194, Thr167, and Thr226. From the results obtained from molecular dynamics, it was observed that one of the loop regions, corresponding to the residues 195-222, can be related to the fitting of the substrate at the binding site, assisting in the positioning and the molecular recognition via residues responsible for the catalytic activity. Conclusion:: he use of molecular modeling techniques enabled the identification of promising compounds as inhibitors of the GAPDH enzyme from L. mexicana, and the results obtained here can serve as a starting point to design new and more effective compounds than those currently available.

scholarly journals Based on Principles and Insights of COVID-19 Epidemiology, Genome Sequencing, and Pathogenesis: Retrospective Analysis of Sinigrin and ProlixinRX (Fluphenazine) Provides Off-Label Drug Candidates

2020 ◽  
Vol 25 (10) ◽  
pp. 1123-1140
Author(s):  
Jilan Nazeam ◽  
Esraa Z. Mohammed ◽  
Mariam Raafat ◽  
Mariam Houssein ◽  
Asmaa Elkafoury ◽  
...  
Keyword(s):  
Natural Products ◽  
Evidence Synthesis ◽  
Drug Repurposing ◽  
New Drugs ◽  
Future Research ◽  
Nitrogenous Compounds ◽  
Future Research Agenda ◽  
Starting Point

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative pathogen of pandemic coronavirus disease 2019 (COVID-19). So far, no approved therapy has been developed to halt the spread of the pathogen, and unfortunately, the strategies for developing a new therapy will require a long time and very extensive resources. Therefore, drug repurposing has emerged as an ideal strategy toward a smart, versatile, quick way to confine the lethal disease. In this endeavor, natural products have been an untapped source for new drugs. This review represents the confederated experience of multidisciplinary researchers of 99 articles using several databases: Google Scholar, Science Direct, MEDLINE, Web of Science, Scopus, and PubMed. To establish the hypothesis, a Bayesian perspective of a systematic review was used to outline evidence synthesis. Our docking documentation of 69 compounds and future research agenda assumptions were directed toward finding an effective and economic anti-COVID-19 treatment from natural products. Glucosinolate, flavones, and sulfated nitrogenous compounds demonstrate direct anti-SARS-CoV-2 activity through inhibition protease enzymes and may be considered potential candidates against coronavirus. These findings could be a starting point to initiate an integrative study that may encompass interested scientists and research institutes to test the hypothesis in vitro, in vivo, and in clinics after satisfying all ethical requirements.

scholarly journals Susceptibility Testing of Medically Important Parasites

2017 ◽  
Vol 30 (3) ◽  
pp. 647-669 ◽  
Author(s):  
Abebe Genetu Bayih ◽  
Anjan Debnath ◽  
Edward Mitre ◽  
Christopher D. Huston ◽  
Benoît Laleu ◽  
...  
Keyword(s):  
Susceptibility Testing ◽  
Neglected Tropical Diseases ◽  
State Of The Art ◽  
Life Cycles ◽  
Point Of View ◽  
New Drugs ◽  
Screening Methods ◽  
Laboratory Methods ◽  
Antiparasitic Agents

SUMMARY In the last 2 decades, renewed attention to neglected tropical diseases (NTDs) has spurred the development of antiparasitic agents, especially in light of emerging drug resistance. The need for new drugs has required in vitro screening methods using parasite culture. Furthermore, clinical laboratories sought to correlate in vitro susceptibility methods with treatment outcomes, most notably with malaria. Parasites with their various life cycles present greater complexity than bacteria, for which standardized susceptibility methods exist. This review catalogs the state-of-the-art methodologies used to evaluate the effects of drugs on key human parasites from the point of view of drug discovery as well as the need for laboratory methods that correlate with clinical outcomes.

scholarly journals The Role of the Cell Volume-Area Ratio in Thermodynamic Analysis of the Cancer Growth Control for In Vitro Experiments

2018 ◽  
Author(s):  
Umberto Lucia ◽  
Giulia Grisolia
Keyword(s):  
Growth Control ◽  
Area Ratio ◽  
Point Of View ◽  
Cancer Growth ◽  
Cyclic Process ◽  
Cell Life ◽  
Starting Point ◽  
Cell Changes

From a thermodynamic point of view, living cell life is no more than a cyclic process. It starts with the newly separated daughter cells and restarts when the next generations grow as free entities. In this cycle the cell changes its entropy. In cancer the growth control is damaged. In this paper we analyze the role of the volume-area ratio in cell in relation to the heat exchange between cell and its environment in order to point out the effect on the cancer growth. The result holds to a possible control of the cancer growth based on the heat exchanged by the cancer towards its environment, and the membrane potential variation, with the consequence of controlling the ions fluxes and the related biochemical reactions. This second law approach could represent a starting point for a possible future support for the anticancer therapies, in order to improve their effectiveness for the untreatable cancers.

scholarly journals In VitroActivity of Fluorescent Dyes against Asexual Blood Stages of Plasmodium falciparum

2012 ◽  
Vol 56 (11) ◽  
pp. 5982-5985 ◽  
Author(s):  
Fanny Joanny ◽  
Jana Held ◽  
Benjamin Mordmüller
Keyword(s):  
Plasmodium Falciparum ◽  
Fluorescent Dyes ◽  
New Drugs ◽  
Synthetic Dyes ◽  
Antimicrobial Drugs ◽  
Content Type ◽  
Starting Point ◽  
Drug Sensitivity Assay ◽  
Syto 9

ABSTRACTMany successful antimicrobial drugs originate from synthetic dyes. This paper reports thein vitroactivity of 14 fluorescent dyes againstPlasmodium falciparum. Five of these dyes (Hoechst 33342, MitoRed, DiOC6, SYTO 9, and rhodamine B) show activity at a low nanomolar concentration against twoP. falciparumstrains in the histidine-rich protein 2 drug sensitivity assay, while toxicity in HeLa cells is low. These dyes may be a starting point for developing new drugs againstP. falciparum.

scholarly journals Searching Hit Potential Antimicrobials in Natural Compounds Space Against Biofilm Formation

2020 ◽  
Author(s):  
Roberto Pestana ◽  
Jorge Leyva ◽  
Juvenal Yosa
Keyword(s):  
Biofilm Formation ◽  
Potential Method ◽  
New Drugs ◽  
Resistant Bacteria ◽  
Chronic Infections ◽  
Aconitic Acid ◽  
Starting Point ◽  
In Silico Studies ◽  
Biofilm Development

Biofilms are communities of microorganisms that can colonize biotic and abiotic surfaces playing a significant role in the persistence of bacterial infection and antibiotic resistance. About 65% and 80% of microbial and chronic infections are produced by biofilm formation. The increase in infections by multi-resistant bacteria draws attention to the discovery of new drugs based on natural inhibitory molecules. The inhibition of diguanylate cyclases (DGCs), the enzyme implicated in the synthesis of the second messenger, cyclic diguanylate (c-di-GMP), involved the biofilm formation, represents a potential method for preventing the biofilm development. It has been extensively studied using PleD protein as a model of DGC for in silico studies as virtual screening and as a model for in vitro studies in biofilms formation. In the present study 224205 molecules from natural products database, ZINC15 has been evaluated through molecular docking and molecular dynamic simulation, our result suggests trans-Aconitic acid (TAA) as a possible starting point for hit-to-lead methodologies to obtain new molecules capable of inhibiting the PleD protein and hence blocking the biofilm formation.

Melanoma Cell Lines Role in Obtaining New Drug Candidates for Combating the Malignant Pathology of the Cutaneous Organ

2019 ◽  
Vol 70 (3) ◽  
pp. 943-945
Author(s):  
Zsolt Gyori ◽  
Monica Susan ◽  
Razvan Susan ◽  
Andrada Iftode ◽  
Cristina Trandafirescu ◽  
...  
Keyword(s):  
Cell Lines ◽  
Point Of View ◽  
In Vitro Studies ◽  
Drug Candidates ◽  
Starting Point ◽  
In Vivo Animal Models ◽  
Culture Growth ◽  
Cell Culture Growth

As prophylactic and therapeutic approaches for melanoma, of great interest and importance are the in vitro studies using cell lines to elucidate several tumoral phenomena. Therefore, the similarities and differences between the different tumor cells must be known and understood in order to obtain a more accurate correlation with processes that occur in vivo. In this study, six cell lines of melanoma, both of mouse and human origin were analyzed from the point of view of cell culture growth, morphology and use in the research of new therapies. In brief, the current paper exhibits a comparison of melanoma cells which can be utilized as a starting point for further in vitro studies and in vivo animal models.

scholarly journals The Role of the Cell Volume-Area Ratio in Thermodynamic Analysis of the Cancer Growth Control for In Vitro Experiments

2018 ◽  
Author(s):  
Umberto Lucia ◽  
Giulia Grisolia
Keyword(s):  
Growth Control ◽  
Area Ratio ◽  
Point Of View ◽  
Cancer Growth ◽  
Cyclic Process ◽  
Cell Life ◽  
Starting Point ◽  
Cell Changes

From a thermodynamic point of view, living cell life is no more than a cyclic process. It starts with the newly separated daughter cells and restarts when the next generations grow as free entities. In this cycle the cell changes its entropy. In cancer the growth control is damaged. In this paper we analyze the role of the volume-area ratio in cell in relation to the heat exchange between cell and its environment in order to point out the effect on the cancer growth. The result holds to a possible control of the cancer growth based on the heat exchanged by the cancer towards its environment, and the membrane potential variation, with the consequence of controlling the ions fluxes and the related biochemical reactions. This second law approach could represent a starting point for a possible future support for the anticancer therapies, in order to improve their effectiveness for the untreatable cancers.

Two isoprenylated flavonoids from Dorstenia psilurus activate AMPK, stimulate glucose uptake, inhibit glucose production and lower glycemia

2019 ◽  
Vol 476 (24) ◽  
pp. 3687-3704 ◽  
Author(s):  
Aphrodite T. Choumessi ◽  
Manuel Johanns ◽  
Claire Beaufay ◽  
Marie-France Herent ◽  
Vincent Stroobant ◽  
...  
Keyword(s):  
Glucose Uptake ◽  
Human Cancer ◽  
Glucose Production ◽  
Liver Mitochondria ◽  
New Drugs ◽  
Structural Isomer ◽  
Rat Liver Mitochondria ◽  
Ionization Mass ◽  
Ampk Activation ◽  
Starting Point

Root extracts of a Cameroon medicinal plant, Dorstenia psilurus, were purified by screening for AMP-activated protein kinase (AMPK) activation in incubated mouse embryo fibroblasts (MEFs). Two isoprenylated flavones that activated AMPK were isolated. Compound 1 was identified as artelasticin by high-resolution electrospray ionization mass spectrometry and 2D-NMR while its structural isomer, compound 2, was isolated for the first time and differed only by the position of one double bond on one isoprenyl substituent. Treatment of MEFs with purified compound 1 or compound 2 led to rapid and robust AMPK activation at low micromolar concentrations and increased the intracellular AMP:ATP ratio. In oxygen consumption experiments on isolated rat liver mitochondria, compound 1 and compound 2 inhibited complex II of the electron transport chain and in freeze–thawed mitochondria succinate dehydrogenase was inhibited. In incubated rat skeletal muscles, both compounds activated AMPK and stimulated glucose uptake. Moreover, these effects were lost in muscles pre-incubated with AMPK inhibitor SBI-0206965, suggesting AMPK dependency. Incubation of mouse hepatocytes with compound 1 or compound 2 led to AMPK activation, but glucose production was decreased in hepatocytes from both wild-type and AMPKβ1−/− mice, suggesting that this effect was not AMPK-dependent. However, when administered intraperitoneally to high-fat diet-induced insulin-resistant mice, compound 1 and compound 2 had blood glucose-lowering effects. In addition, compound 1 and compound 2 reduced the viability of several human cancer cells in culture. The flavonoids we have identified could be a starting point for the development of new drugs to treat type 2 diabetes.

Sign in / Sign up

Export Citation Format

Share Document