scholarly journals In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function

Catalysts ◽  
2017 ◽  
Vol 7 (7) ◽  
pp. 212 ◽  
Author(s):  
◽  
Keyword(s):  
Small Molecule ◽  
In Silico ◽  
Catalytic Function ◽  
In Silico Studies ◽  
Molecule Interactions

scholarly journals Nature as a Treasure Trove for Anti-COVID-19: Luteolin and Naringenin from Indonesian Traditional Herbal Medicine Reveal Potential SARS-CoV-2 Mpro Inhibitors Insight from in Silico Studies

2020 ◽  
Author(s):  
Wahyu Prasetyo ◽  
Triana Kusumaningsih ◽  
Maulidan Firdaus
Keyword(s):  
Chinese Medicine ◽  
Herbal Medicine ◽  
Traditional Chinese Medicine ◽  
Medicinal Plants ◽  
Small Molecule ◽  
In Silico ◽  
Dft Studies ◽  
Traditional Herbal Medicine ◽  
In Silico Studies ◽  
Bioactive Phytochemicals

<div>Since the worldwide is currently facing the COVID-19 pandemic, there are no drugs or vaccines have been approved</div><div>for the treatment of SARS-CoV-2 infection. Therefore, there is an urgent need for in-depth research on emerging</div><div>human infectious coronaviruses. As part of our endeavour in combating this COVID-19 pandemic, in this paper, we</div><div>report on the discovery of an active antiviral small-molecule from Indonesian traditional herbal medicine used in Jamu</div><div>to inhibit 3CLpro of SARS-CoV-2 using in-silico approaches. As one of the mega biodiversity countries, Indonesia has</div><div>more than 1,180 species that can be prospected for medicine plants. Jamu, the Indonesian traditional herbal medicine,</div><div>is supposed to have similar potentials as those of traditional Chinese medicine (TCM). However, due to the lack of</div><div>scientific proof, Jamu is not recognised in the Guideline of COVID-19 Patients, particularly in Indonesia. Thus, in</div><div>this study, we performed virtual docking screening along with pharmacokinetic and DFT studies of selected 49</div><div>bioactive phytochemicals from several medicinal plants used in Jamu against the 3CLpro enzyme of SARS-CoV-2.</div><div>From the result, it was noted that from a set of 49 phytochemicals of medicinal plants used in Jamu, 2 phytochemicals,</div><div>i.e., Luteolin and Naringenin were identified as potential druggable inhibitors candidates of 3CLpro of SARS CoV-2.</div>

scholarly journals Template Instrumentation for "Accurate Constant via Transient Incomplete Separation" (ACTIS)

2021 ◽  
Author(s):  
Jean-Luc Rukundo ◽  
Sven Kochmann ◽  
Tong Ye Wang ◽  
Nikita A. Ivanov ◽  
J.C. Yves Le Blanc ◽  
...  
Keyword(s):  
Small Molecule ◽  
In Silico ◽  
Diffusion Processes ◽  
Equilibrium Dissociation Constant ◽  
Transverse Diffusion ◽  
Advection Diffusion ◽  
In Silico Studies ◽  
Equilibrium Dissociation ◽  
Pressure Driven Flow ◽  
System Geometry

<p>ACTIS is a new method for finding the equilibrium dissociation constant <i>K</i><sub>d</sub> of a protein–small molecule complex based on transient incomplete separation of the complex from the unbound small molecule in a capillary. This separation is caused by differential transverse diffusion of the complex and the small molecule in a pressure-driven flow. The advection-diffusion processes underlying ACTIS can be described by a system of partial differential equations allowing for a virtual ACTIS instrument to be built and ACTIS to be studied in silico. The previous in-silico studies show that large variations in the fluidic system geometry do not affect the accuracy of <i>K</i><sub>d</sub> determination, thus, proving that ACTIS is conceptually accurate. The conceptual accuracy does not preclude, however, instrumental inaccuracy caused by run-to-run signal drifts. Here we report on assembling a physical ACTIS instrument with a fluidic system that mimics the virtual one and proving the absence of signal drifts. Furthermore, we confirmed method ruggedness by assembling a second ACTIS instrument and comparing the results of experiments performed with both instruments in parallel. Despite some differences between the instruments and, accordingly, significant differences in their respective separagrams, we found that the <i>K</i><sub>d</sub> values determined for identical samples with these instruments were equal. Conclusively, the fluidic system presented here can serve as a template for reliable ACTIS instrumentation.</p>

scholarly journals Nature as a Treasure Trove for Anti-COVID-19: Luteolin and Naringenin from Indonesian Traditional Herbal Medicine Reveal Potential SARS-CoV-2 Mpro Inhibitors Insight from in Silico Studies

2020 ◽  
Author(s):  
Wahyu Prasetyo ◽  
Triana Kusumaningsih ◽  
Maulidan Firdaus
Keyword(s):  
Chinese Medicine ◽  
Herbal Medicine ◽  
Traditional Chinese Medicine ◽  
Medicinal Plants ◽  
Small Molecule ◽  
In Silico ◽  
Dft Studies ◽  
Traditional Herbal Medicine ◽  
In Silico Studies ◽  
Bioactive Phytochemicals

<div>Since the worldwide is currently facing the COVID-19 pandemic, there are no drugs or vaccines have been approved</div><div>for the treatment of SARS-CoV-2 infection. Therefore, there is an urgent need for in-depth research on emerging</div><div>human infectious coronaviruses. As part of our endeavour in combating this COVID-19 pandemic, in this paper, we</div><div>report on the discovery of an active antiviral small-molecule from Indonesian traditional herbal medicine used in Jamu</div><div>to inhibit 3CLpro of SARS-CoV-2 using in-silico approaches. As one of the mega biodiversity countries, Indonesia has</div><div>more than 1,180 species that can be prospected for medicine plants. Jamu, the Indonesian traditional herbal medicine,</div><div>is supposed to have similar potentials as those of traditional Chinese medicine (TCM). However, due to the lack of</div><div>scientific proof, Jamu is not recognised in the Guideline of COVID-19 Patients, particularly in Indonesia. Thus, in</div><div>this study, we performed virtual docking screening along with pharmacokinetic and DFT studies of selected 49</div><div>bioactive phytochemicals from several medicinal plants used in Jamu against the 3CLpro enzyme of SARS-CoV-2.</div><div>From the result, it was noted that from a set of 49 phytochemicals of medicinal plants used in Jamu, 2 phytochemicals,</div><div>i.e., Luteolin and Naringenin were identified as potential druggable inhibitors candidates of 3CLpro of SARS CoV-2.</div>

scholarly journals Template Instrumentation for "Accurate Constant via Transient Incomplete Separation" (ACTIS)

2021 ◽  
Author(s):  
Jean-Luc Rukundo ◽  
Sven Kochmann ◽  
Tong Ye Wang ◽  
Nikita A. Ivanov ◽  
J.C. Yves Le Blanc ◽  
...  
Keyword(s):  
Small Molecule ◽  
In Silico ◽  
Diffusion Processes ◽  
Equilibrium Dissociation Constant ◽  
Transverse Diffusion ◽  
Advection Diffusion ◽  
In Silico Studies ◽  
Equilibrium Dissociation ◽  
Pressure Driven Flow ◽  
System Geometry

<p>ACTIS is a new method for finding the equilibrium dissociation constant <i>K</i><sub>d</sub> of a protein–small molecule complex based on transient incomplete separation of the complex from the unbound small molecule in a capillary. This separation is caused by differential transverse diffusion of the complex and the small molecule in a pressure-driven flow. The advection-diffusion processes underlying ACTIS can be described by a system of partial differential equations allowing for a virtual ACTIS instrument to be built and ACTIS to be studied in silico. The previous in-silico studies show that large variations in the fluidic system geometry do not affect the accuracy of <i>K</i><sub>d</sub> determination, thus, proving that ACTIS is conceptually accurate. The conceptual accuracy does not preclude, however, instrumental inaccuracy caused by run-to-run signal drifts. Here we report on assembling a physical ACTIS instrument with a fluidic system that mimics the virtual one and proving the absence of signal drifts. Furthermore, we confirmed method ruggedness by assembling a second ACTIS instrument and comparing the results of experiments performed with both instruments in parallel. Despite some differences between the instruments and, accordingly, significant differences in their respective separagrams, we found that the <i>K</i><sub>d</sub> values determined for identical samples with these instruments were equal. Conclusively, the fluidic system presented here can serve as a template for reliable ACTIS instrumentation.</p>

Critical Review on the Chemical Aspects of Cannabidiol (CBD) and Harmonization of Computational Bioactivity Data

2020 ◽  
Vol 28 (2) ◽  
pp. 213-237 ◽  
Author(s):  
Andrea Mastinu ◽  
Giovanni Ribaudo ◽  
Alberto Ongaro ◽  
Sara Anna Bonini ◽  
Maurizio Memo ◽  
...  
Keyword(s):  
In Silico ◽  
Cannabis Sativa ◽  
Therapeutic Potential ◽  
The Novel ◽  
In Silico Studies ◽  
Computational Data ◽  
Synthetic Approaches ◽  
Analytical Approaches ◽  
Yield Sensitivity ◽  
Therapeutic Profile

: Cannabidiol (CBD) is a non-psychotropic phytocannabinoid which represents one of the constituents of the “phytocomplex” of Cannabis sativa. This natural compound is attracting growing interest since when CBD-based remedies and commercial products were marketed. This review aims to exhaustively address the extractive and analytical approaches that have been developed for the isolation and quantification of CBD. Recent updates on cutting-edge technologies were critically examined in terms of yield, sensitivity, flexibility and performances in general, and are reviewed alongside original representative results. As an add-on to currently available contributions in the literature, the evolution of the novel, efficient synthetic approaches for the preparation of CBD, a procedure which is appealing for the pharmaceutical industry, is also discussed. Moreover, with the increasing interest on the therapeutic potential of CBD and the limited understanding of the undergoing biochemical pathways, the reader will be updated about recent in silico studies on the molecular interactions of CBD towards several different targets attempting to fill this gap. Computational data retrieved from the literature have been integrated with novel in silico experiments, critically discussed to provide a comprehensive and updated overview on the undebatable potential of CBD and its therapeutic profile.

Recent In Vitro and In Silico Advances in the Understanding of Intranasal Drug Delivery

2020 ◽  
Vol 26 ◽  
Author(s):  
John Chen ◽  
Andrew Martin ◽  
Warren H. Finlay
Keyword(s):  
Drug Delivery ◽  
In Silico ◽  
Local Drug Delivery ◽  
In Vivo Studies ◽  
Intranasal Drug Delivery ◽  
Nasal Sprays ◽  
In Silico Studies ◽  
Drug Delivery Devices

Background: Many drugs are delivered intranasally for local or systemic effect, typically in the form of droplets or aerosols. Because of the high cost of in vivo studies, drug developers and researchers often turn to in vitro or in silico testing when first evaluating the behavior and properties of intranasal drug delivery devices and formulations. Recent advances in manufacturing and computer technologies have allowed for increasingly realistic and sophisticated in vitro and in silico reconstructions of the human nasal airways. Objective: To perform a summary of advances in understanding of intranasal drug delivery based on recent in vitro and in silico studies. Conclusion: The turbinates are a common target for local drug delivery applications, and while nasal sprays are able to reach this region, there is currently no broad consensus across the in vitro and in silico literature concerning optimal parameters for device design, formulation properties and patient technique which would maximize turbinate deposition. Nebulizers are able to more easily target the turbinates, but come with the disadvantage of significant lung deposition. Targeting of the olfactory region of the nasal cavity has been explored for potential treatment of central nervous system conditions. Conventional intranasal devices, such as nasal sprays and nebulizers, deliver very little dose to the olfactory region. Recent progress in our understanding of intranasal delivery will be useful in the development of the next generation of intranasal drug delivery devices.

In-silico Studies of Isolated Phytoalkaloid Against Lipoxygenase: Study Based on Possible Correlation

2018 ◽  
Vol 21 (3) ◽  
pp. 215-221
Author(s):  
Haroon Khan ◽  
Muhammad Zafar ◽  
Helena Den-Haan ◽  
Horacio Perez-Sanchez ◽  
Mohammad Amjad Kamal
Keyword(s):  
In Silico ◽  
Docking Studies ◽  
In Vivo Studies ◽  
In Vitro Assays ◽  
Chronic Obstructive ◽  
Lipoxygenase Inhibitors ◽  
Lipoxygenase Inhibition ◽  
In Silico Studies

Aim and Objective: Lipoxygenase (LOX) enzymes play an important role in the pathophysiology of several inflammatory and allergic diseases including bronchial asthma, allergic rhinitis, atopic dermatitis, allergic conjunctivitis, rheumatoid arthritis and chronic obstructive pulmonary disease. Inhibitors of the LOX are believed to be an ideal approach in the treatment of diseases caused by its over-expression. In this regard, several synthetic and natural agents are under investigation worldwide. Alkaloids are the most thoroughly investigated class of natural compounds with outstanding past in clinically useful drugs. In this article, we have discussed various alkaloids of plant origin that have already shown lipoxygenase inhibition in-vitro with possible correlation in in silico studies. Materials and Methods: Molecular docking studies were performed using MOE (Molecular Operating Environment) software. Among the ten reported LOX alkaloids inhibitors, derived from plant, compounds 4, 2, 3 and 1 showed excellent docking scores and receptor sensitivity. Result and Conclusion: These compounds already exhibited in vitro lipoxygenase inhibition and the MOE results strongly correlated with the experimental results. On the basis of these in vitro assays and computer aided results, we suggest that these compounds need further detail in vivo studies and clinical trial for the discovery of new more effective and safe lipoxygenase inhibitors. In conclusion, these results might be useful in the design of new and potential lipoxygenase (LOX) inhibitors.

Promising Anticancer Therapeutics From Mushrooms: Current Findings and Future Perceptions

2020 ◽  
Vol 21 ◽  
Author(s):  
Mrunmaya Kumar Panda ◽  
Manish Paul ◽  
Sameer Kumar Singdevsachan ◽  
Kumananda Tayung ◽  
Swagat Kumar Das ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Cancer Cell ◽  
In Silico ◽  
Present Review ◽  
Cancer Cell Proliferation ◽  
Research Papers ◽  
Medicinal Mushrooms ◽  
In Silico Studies ◽  
Anticancer Therapeutics ◽  
Ethnomedicinal Uses

Background: Nowadays medicines derived from natural sources have drawn much attention as potential therapeutic agents in the suppression and treatment of cancer because of their low toxicity and fewer side effects. Objective: The present review aims to assess the currently available knowledge on the ethnomedicinal uses and pharmacological activities of bioactive compounds obtained from medicinal mushrooms towards cancer treatment. Methods: Literature search has been conducted for the collection of research papers from universally accepted scientific databases. These research papers and published book chapters were scrutinized to retrieve information on ethnomedicinal uses of mushrooms, different factors involved in cancer cell proliferation, clinical and in silico pharmaceutical studies made for possible treatments of cancer using mushroom derived compounds. Overall 241 articles were retrieved and reviewed from the year of 1970 to 2020, out of which 98 relevant articles were finally considered for preparation of this review. Results: This review presents an update on the natural bioactive substances derived from medicinal mushrooms and their role in inhibiting the factors responsible for cancer cell proliferation. Along with it, the present review also provides information on the ethnomedicinal uses, solvents used for extraction of anticancer metabolites, clinical trials, and in silico studies that were undertaken towards anticancer drug development from medicinal mushrooms. Conclusion: The present review provides an extensive knowledge on various anticancer substances obtained from medicinal mushrooms, their biological actions and in silico drug designing approaches which could form a basis for the development of natural anticancer therapeutics.

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