scholarly journals Identification of Kaurane-Type Diterpenes as Inhibitors of Leishmania Pteridine Reductase I

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3076
Author(s):  
Chonny Herrera-Acevedo ◽  
Areli Flores-Gaspar ◽  
Luciana Scotti ◽  
Francisco Jaime Bezerra Mendonça-Junior ◽  
Marcus Tullius Scotti ◽  
...  
Keyword(s):  
Active Sites ◽  
Leishmania Major ◽  
Inhibitory Concentration ◽  
Chemical Space ◽  
Leishmania Species ◽  
Ic50 Values ◽  
Docking Calculations ◽  
Dynamics Simulations ◽  
Potential Inhibitors ◽  
Leishmania Parasites

The current treatments against Leishmania parasites present high toxicity and multiple side effects, which makes the control and elimination of leishmaniasis challenging. Natural products constitute an interesting and diverse chemical space for the identification of new antileishmanial drugs. To identify new drug options, an in-house database of 360 kauranes (tetracyclic diterpenes) was generated, and a combined ligand- and structure-based virtual screening (VS) approach was performed to select potential inhibitors of Leishmania major (Lm) pteridine reductase I (PTR1). The best-ranked kauranes were employed to verify the validity of the VS approach through LmPTR1 enzyme inhibition assay. The half-maximal inhibitory concentration (IC50) values of selected bioactive compounds were examined using the random forest (RF) model (i.e., 2β-hydroxy-menth-6-en-5β-yl ent-kaurenoate (135) and 3α-cinnamoyloxy-ent-kaur-16-en-19-oic acid (302)) were below 10 μM. A compound similar to 302, 3α-p-coumaroyloxy-ent-kaur-16-en-19-oic acid (302a), was also synthesized and showed the highest activity against LmPTR1. Finally, molecular docking calculations and molecular dynamics simulations were performed for the VS-selected, most-active kauranes within the active sites of PTR1 hybrid models, generated from three Leishmania species that are known to cause cutaneous leishmaniasis in the new world (i.e., L. braziliensis, L. panamensis, and L. amazonensis) to explore the targeting potential of these kauranes to other species-dependent variants of this enzyme.

scholarly journals 3-Methoxycarpachromene and Masticadienonic Acid as New Target Inhibitors from Pistacia atlantica Leaves against Trypanothione Reductase of Leishmania Parasites: In Vitro and In Silico Studies

2021 ◽  
Author(s):  
Saarra Maamri ◽  
Khedidja Benarous ◽  
Mohamed Yousfi
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Leishmania Major ◽  
Trypanothione Reductase ◽  
Binding Modes ◽  
Pistacia Atlantica ◽  
In Silico Studies ◽  
Ic50 Values ◽  
Leishmania Parasites

This study aimed to identify new drug molecules against Leishmania parasites, leishmaniasis's causal agent, using Pistacia atlantica leaves as source. The evaluation of the anti-leishmania potential against the promastigote form of Leishmania. infantum and Leishmania. major was performed. A new in silico study was accomplished using molecular docking, with Autodock vina program, to find the binding affinity of two important phytochemical compounds from this plant (Masticadienonic acid, 3-Methoxycarpachromene) towards the trypanothione reductase as target drugs, responsible for defence mechanism against oxidative stress and virulence of this parasites. Results: Several concentrations showed a significant decrease in cell viability (P<0.0001), with IC50 values of 0.3 mg/ mL for L. infantum and 0.12 mg/ mL L. major; The molecular docking confirms the significant relationship between Leishmania survival and the inhibition of this crucial enzyme. There were promising and new positive results on binding modes of selected ligands and the trypanothione reductase for the first time. Through this work, we propose 3-Methoxycarpachromene and Masticadienonic acid as anti Trypanosomatidae species drug.

scholarly journals In Silico Studies of Potential Selective Inhibitors of Thymidylate Kinase from Variola virus

2021 ◽  
Vol 14 (10) ◽  
pp. 1027
Author(s):  
Danielle R. Garcia ◽  
Felipe R. Souza ◽  
Ana P. Guimarães ◽  
Martin Valis ◽  
Zbyšek Pavelek ◽  
...  
Keyword(s):  
Free Energy ◽  
Active Sites ◽  
Free Energy Calculations ◽  
Variola Virus ◽  
Selective Inhibitors ◽  
Thymidylate Kinase ◽  
In Silico Studies ◽  
Docking Calculations ◽  
Poisson Boltzmann ◽  
Dynamics Simulations

Continuing the work developed by our research group, in the present manuscript, we performed a theoretical study of 10 new structures derived from the antivirals cidofovir and ribavirin, as inhibitor prototypes for the enzyme thymidylate kinase from Variola virus (VarTMPK). The proposed structures were subjected to docking calculations, molecular dynamics simulations, and free energy calculations, using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method, inside the active sites of VarTMPK and human TMPK (HssTMPK). The docking and molecular dynamic studies pointed to structures 2, 3, 4, 6, and 9 as more selective towards VarTMPK. In addition, the free energy data calculated through the MM-PBSA method, corroborated these results. This suggests that these compounds are potential selective inhibitors of VarTMPK and, thus, can be considered as template molecules to be synthesized and experimentally evaluated against smallpox.

scholarly journals Potential Inhibitors for Novel Coronavirus Protease Identified by Virtual Screening of 606 Million Compounds

2020 ◽  
Vol 21 (10) ◽  
pp. 3626 ◽  
Author(s):  
André Fischer ◽  
Manuel Sellner ◽  
Santhosh Neranjan ◽  
Martin Smieško ◽  
Markus A. Lill
Keyword(s):  
Viral Infections ◽  
Chemical Space ◽  
Drug Repurposing ◽  
Close Relation ◽  
Binding Energies ◽  
Proteolytic Processing ◽  
Binding Modes ◽  
Novel Coronavirus ◽  
Dynamics Simulations ◽  
Potential Inhibitors

The rapid outbreak of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China followed by its spread around the world poses a serious global concern for public health. To this date, no specific drugs or vaccines are available to treat SARS-CoV-2 despite its close relation to the SARS-CoV virus that caused a similar epidemic in 2003. Thus, there remains an urgent need for the identification and development of specific antiviral therapeutics against SARS-CoV-2. To conquer viral infections, the inhibition of proteases essential for proteolytic processing of viral polyproteins is a conventional therapeutic strategy. In order to find novel inhibitors, we computationally screened a compound library of over 606 million compounds for binding at the recently solved crystal structure of the main protease (Mpro) of SARS-CoV-2. A screening of such a vast chemical space for SARS-CoV-2 Mpro inhibitors has not been reported before. After shape screening, two docking protocols were applied followed by the determination of molecular descriptors relevant for pharmacokinetics to narrow down the number of initial hits. Next, molecular dynamics simulations were conducted to validate the stability of docked binding modes and comprehensively quantify ligand binding energies. After evaluation of potential off-target binding, we report a list of 12 purchasable compounds, with binding affinity to the target protease that is predicted to be more favorable than that of the cocrystallized peptidomimetic compound. In order to quickly advise ongoing therapeutic intervention for patients, we evaluated approved antiviral drugs and other protease inhibitors to provide a list of nine compounds for drug repurposing. Furthermore, we identified the natural compounds (−)-taxifolin and rhamnetin as potential inhibitors of Mpro. Rhamnetin is already commercially available in pharmacies.

scholarly journals Molecular Identification of Leishmania Species in Phlebotomus alexandri (Diptera: Psychodidae) in Western Iran

2020 ◽  
Author(s):  
Abdollah Naghian ◽  
Mohammad Ali Oshaghi ◽  
Vahideh Moein-Vaziri ◽  
Yavar Rassi ◽  
Mohammad Mehdi Sedaghat ◽  
...  
Keyword(s):  
Nested Pcr ◽  
Leishmania Donovani ◽  
Leishmania Major ◽  
Leishmania Species ◽  
Fars Province ◽  
Sand Flies ◽  
Khuzestan Province ◽  
East Azerbaijan ◽  
Pooled Samples ◽  
Leishmania Parasites

Background: Visceral and cutaneous leishmaniasis are common in some areas of Iran and consider as health problems. Phlebotomus alexandri has been incriminated as a suspected vector for the both form of leishmaniasis. Methods: This study was carried out in 4 western provinces of Iran. Sand flies were collected using sticky traps and light traps from indoor and outdoor resting places. Nested PCR was employed to detect Leishmania parasites among collected sand flies. Results: Seven hundred and twenty two P. alexandri females were collected and pooled in 179 batches. Results of nested PCR showed, out of 9 samples from East Azerbaijan Province, only one sample was infected by Leishmania infantum. Of 34 individual and pooled samples from Kermanshah Province, only one pooled sample was infected with Leishmania major and among 30 individual and pooled samples in Fars Province, five specimens were infected by L. major, L. infantum, Leishmania donovani and Leishmania tropica. Furthermore, out of 108 individual and pooled samples from Khuzestan Province, 10 samples showed infection with L. major and L. infantum. Conclusion: The results of this study showed that P. alexandri is more active in hot zones than in moderate zones and this species may be considered as a permissive species.

scholarly journals Piperazine-based HIV-1 entry inhibitors: Massive in silico library design and screening for gp120 attachment inhibitors

2018 ◽  
Author(s):  
Durbis J. Castillo-Pazos ◽  
Antonio Romo-Mancillas ◽  
Joaquín Barroso-Flores
Keyword(s):  
Highly Active Antiretroviral Therapy ◽  
Chemical Space ◽  
Library Design ◽  
Promising Candidate ◽  
Entry Inhibitors ◽  
Highly Active ◽  
Gp120 Envelope ◽  
Docking Calculations ◽  
Dynamics Simulations ◽  
Hiv 1

ABSTRACTHIV-1 attachment, despite being an ideal target stage to stop infection from the beginning, remains as one of the HIV lifecycle phases with less amount of designed and commercially available inhibitors. To contribute to the urgently needed discovery of new active compounds that could become part of the current highly active antiretroviral therapy, and as an attempt to explore a massive chemical space, high-throughput virtual screening of 16.3 million combinatorially generated and piperazine-cored compounds, was accomplished. Docking calculations, molecular dynamics simulations, and QSAR analyses were carried out to assess the suitability of each ligand to bind gp120 envelope glycoprotein, thus preventing it from binding to CD4 co-receptor. Ligand 255 stands out as a promising candidate to be tested beyond computational methodologies, and the 4,5,6,7-tetrahydroindole fragment is reported as a better group to bind inside the Phe43 cavity than the substituted indoles reported in the literature.

Effects of Folpet, Captan, and Captafol on Human Aromatase in JEG-3 Cells

Pharmacology ◽  
2018 ◽  
Vol 102 (1-2) ◽  
pp. 81-87 ◽  
Author(s):  
Hongshan Ge ◽  
Lanlan Chen ◽  
Ying Su ◽  
Chunyan Jin ◽  
Ren-Shan Ge
Keyword(s):  
Inhibitory Concentration ◽  
Simulation Analysis ◽  
Docking Simulation ◽  
Binding Pocket ◽  
Dependent Manner ◽  
Concentration Dependent Manner ◽  
Molecular Docking Simulation ◽  
Ic50 Values ◽  
Steroid Binding ◽  
Potential Inhibitors

Background: Estradiol, produced by aromatase (CYP19A1), is very important for reproduction. Folpet, captan, and captafol belong to the phthalimide class of fungicides. They are used to protect the leaves of plants or fruits. They could be endocrine disruptors and may disrupt CYP19A1 activity. Methods: In the present study, we investigated the effects of folpet, captan, and captafol on estradiol production and human CYP19A1 activity in JEG-3 cells. Results: Folpet, captan, and captafol decreased estradiol production in JEG-3 cells in a concentration-dependent manner. Folpet, captan, and captafol inhibited human CYP19A1 with inhibitory concentration (IC50) values of 3.55, 10.68, and 1.14 μmol/L respectively. These chemicals competitively inhibited human CYP19A1. Molecular docking simulation analysis showed that they tended to bind to the steroid-binding pocket of the CYP19A1. However, the required concentrations may not be relevant to the negligible systemic exposures in humans to these chemicals. Conclusion: Folpet, captan, and captafol are potential inhibitors of human CYP19A1.

scholarly journals Structure-based identification of naphthoquinones and derivatives as novel inhibitors of main protease Mpro and papain-like protease PLpro of SARS-CoV-2

2022 ◽  
Author(s):  
Lucianna H. Santos ◽  
Thales Kronenberger ◽  
Renata G Almeida ◽  
Elany Barbosa da Silva ◽  
Rafael E O Rocha ◽  
...  
Keyword(s):  
Active Site ◽  
Drug Targets ◽  
Inhibitory Concentration ◽  
Binding Modes ◽  
Fluorogenic Substrate ◽  
Biochemical Assays ◽  
Main Protease ◽  
Ic50 Values ◽  
Biochemical Approach ◽  
Dynamics Simulations

The worldwide COVID-19 pandemic caused by the coronavirus SARS-CoV-2 urgently demands novel direct antiviral treatments. The main protease (Mpro) and papain-like protease (PLpro) are attractive drug targets among coronaviruses due to their essential role in processing the polyproteins translated from the viral RNA. In the present work, we virtually screened 688 naphthoquinoidal compounds and derivatives against Mpro of SARS-CoV-2. Twenty-four derivatives were selected and evaluated in biochemical assays against Mpro using a novel fluorogenic substrate. In parallel, these compounds were also assayed with SARS-CoV-2 PLpro. Four compounds inhibited Mpro with half-maximal inhibitory concentration (IC50) values between 0.41 μM and 66 μM. In addition, eight compounds inhibited PLpro with IC50 ranging from 1.7 μM to 46 μM. Molecular dynamics simulations suggest stable binding modes for Mpro inhibitors with frequent interactions with residues in the S1 and S2 pockets of the active site. For two PLpro inhibitors, interactions occur in the S3 and S4 pockets. In summary, our structure-based computational and biochemical approach identified novel naphthoquinonal scaffolds that can be further explored as SARS-CoV-2 antivirals.

On the Adsorption of Aspartate Derivatives to Calcite Surfaces in Aqueous Environment

2020 ◽  
Author(s):  
Robert Stepic ◽  
Lara Jurković ◽  
Ksenia Klementyeva ◽  
Marko Ukrainczyk ◽  
Matija Gredičak ◽  
...  
Keyword(s):  
Active Sites ◽  
Realistic Model ◽  
Binding Energies ◽  
Inhibition Mechanism ◽  
Aqueous Environment ◽  
Binding Modes ◽  
Carboxylate Groups ◽  
Dissolved Ions ◽  
Living Organisms ◽  
Dynamics Simulations

In many living organisms, biomolecules interact favorably with various surfaces of calcium carbonate. In this work, we have considered the interactions of aspartate (Asp) derivatives, as models of complex biomolecules, with calcite. Using kinetic growth experiments, we have investigated the inhibition of calcite growth by Asp, Asp2 and Asp3.This entailed the determination of a step-pinning growth regime as well as the evaluation of the adsorption constants and binding free energies for the three species to calcite crystals. These latter values are compared to free energy profiles obtained from fully atomistic molecular dynamics simulations. When using a flat (104) calcite surface in the models, the measured trend of binding energies is poorly reproduced. However, a more realistic model comprised of a surface with an island containing edges and corners, yields binding energies that compare very well with experiments. Surprisingly, we find that most binding modes involve the positively charged, ammonium group. Moreover, while attachment of the negatively charged carboxylate groups is also frequently observed, it is always balanced by the aqueous solvation of an equal or greater number of carboxylates. These effects are observed on all calcite features including edges and corners, the latter being associated with dominant affinities to Asp derivatives. As these features are also precisely the active sites for crystal growth, the experimental and theoretical results point strongly to a growth inhibition mechanism whereby these sites become blocked, preventing further attachment of dissolved ions and halting further growth.

Towards a Design of Active Oxygen Evolution Catalysts: Insights from Automated Density Functional Theory Calculations and Machine Learning

2019 ◽  
Author(s):  
Seoin Back ◽  
Kevin Tran ◽  
Zachary Ulissi
Keyword(s):  
Machine Learning ◽  
Oxygen Evolution ◽  
Active Sites ◽  
Density Functional ◽  
Chemical Space ◽  
Density Functional Theory Calculations ◽  
Catalyst Design ◽  
Transition Metal Catalysts ◽  
Oxide Materials ◽  
Design Strategies

<div> <div> <div> <div><p>Developing active and stable oxygen evolution catalysts is a key to enabling various future energy technologies and the state-of-the-art catalyst is Ir-containing oxide materials. Understanding oxygen chemistry on oxide materials is significantly more complicated than studying transition metal catalysts for two reasons: the most stable surface coverage under reaction conditions is extremely important but difficult to understand without many detailed calculations, and there are many possible active sites and configurations on O* or OH* covered surfaces. We have developed an automated and high-throughput approach to solve this problem and predict OER overpotentials for arbitrary oxide surfaces. We demonstrate this for a number of previously-unstudied IrO2 and IrO3 polymorphs and their facets. We discovered that low index surfaces of IrO2 other than rutile (110) are more active than the most stable rutile (110), and we identified promising active sites of IrO2 and IrO3 that outperform rutile (110) by 0.2 V in theoretical overpotential. Based on findings from DFT calculations, we pro- vide catalyst design strategies to improve catalytic activity of Ir based catalysts and demonstrate a machine learning model capable of predicting surface coverages and site activity. This work highlights the importance of investigating unexplored chemical space to design promising catalysts.<br></p></div></div></div></div><div><div><div> </div> </div> </div>

Evaluating the Effect of Cinnarizine on Promastigotes and Amastigotes forms of Leishmania major

2020 ◽  
Vol 20 (4) ◽  
pp. 550-555 ◽  
Author(s):  
Lima Asgharpour Sarouey ◽  
Parvaneh Rahimi-Moghaddam ◽  
Fatemeh Tabatabaie ◽  
Khadijeh Khanaliha
Keyword(s):  
Flow Cytometry ◽  
Cutaneous Leishmaniasis ◽  
Leishmania Major ◽  
Inhibitory Effect ◽  
Control Group ◽  
Secondary Infections ◽  
Ic50 Values ◽  
J774 Cells ◽  
Mtt Assays

: As an important global disease, cutaneous leishmaniasis is associated with complications such as secondary infections and atrophic scars. The first line treatment with antimonials is expensive and reported to have serious side effects and enhance resistance development. The main objective of this study was to evaluate the effect of Cinnarizine on standard strains of Leishmania major because of paucity of information on this subject. Methods: In this experimental study, four concentrations of the drug (5, 10, 15 and 20 μg/ml) were added to Leishmania major cultures at 24, 48 and 72 hours intervals. MTT assays were performed to determine parasite viability and drug toxicity. Leishmania major promastigotes were augmented to the in vitro cultured macrophages (J774 cells) and then incubated for 72 hours. Half maximal inhibitory concentration (IC50) was ascertained by counting parasites. The inhibitory effect of the drug was compared with that of Glucantime. Flow-cytometry was performed to investigate apoptosis. Each test was repeated thrice. Results: The IC50 values of Cinnarizine after 72 hours were calculated to be 34.76 μg/ml and 23.73 μg/ml for promastigotes and amastigotes, respectively. The results of MTT assays showed 48 % promastigote viability after 72 hour-exposure to Cinnarizine at 20 μg/ml concentration. Programmed cell death in promastigote- and amastigote-infected macrophages was quantified to be 13.66 % and 98.7 %, respectively. Flow- cytometry analysis indicated that Cinnarizine induced early and late apoptosis in parasites. All treatments produced results which differed significantly from control group (P<0.05). Conclusion: Cinnarizine showed low toxicity with anti-leishmanial and apoptosis effects on both promastigote and intracellular amastigote forms. Therefore, we may suggest further assessment on animal models of this drug as candidates for cutaneous leishmaniasis therapy.

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