Insights into the Structure of Rubisco from Dinoflagellates-in Silico Studies

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is one of the best studied enzymes. It is crucial for photosynthesis, and thus for all of biosphere’s productivity. There are four isoforms of this enzyme, differing by amino acid sequence composition and quaternary structure. However, there is still a group of organisms, dinoflagellates, single-cell eukaryotes, that are confirmed to possess Rubisco, but no successful purification of the enzyme of such origin, and hence a generation of a crystal structure was reported to date. Here, we are using in silico tools to generate the possible structure of Rubisco from a dinoflagellate representative, Symbiodinium sp. We selected two templates: Rubisco from Rhodospirillum rubrum and Rhodopseudomonas palustris. Both enzymes are the so-called form II Rubiscos, but the first is exclusively a homodimer, while the second one forms homo-hexamers. Obtained models show no differences in amino acids crucial for Rubisco activity. The variation was found at two closely located inserts in the C-terminal domain, of which one extends a helix and the other forms a loop. These inserts most probably do not play a direct role in the enzyme’s activity, but may be responsible for interaction with an unknown protein partner, possibly a regulator or a chaperone. Analysis of the possible oligomerization interface indicated that Symbiodinium sp. Rubisco most likely forms a trimer of homodimers, not just a homodimer. This hypothesis was empowered by calculation of binding energies. Additionally, we found that the protein of study is significantly richer in cysteine residues, which may be the cause for its activity loss shortly after cell lysis. Furthermore, we evaluated the influence of the loop insert, identified exclusively in the Symbiodinium sp. protein, on the functionality of the recombinantly expressed R. rubrum Rubisco. All these findings shed new light onto dinoflagellate Rubisco and may help in future obtainment of a native, active enzyme.

Download Full-text

Phytochemicals as Therapeutics Against COVID-19: An In-Silico Study

10.20944/preprints202012.0708.v1 ◽

2020 ◽

Author(s):

Debraj Koiri ◽

Ditam Chakraborty ◽

Pranotosh Das ◽

Rajkumar Rana ◽

Soumyanil Chatterjee ◽

...

Keyword(s):

In Silico ◽

Therapeutic Agents ◽

Binding Energies ◽

Daily Lives ◽

Lab Experiments ◽

In Silico Studies ◽

In Silico Study ◽

The World ◽

Wet Lab ◽

Low Costs

Since December 2019, the worldwide spread of COVID-19 has brought the majority of the world to a standstill, affecting daily lives as well as economy. Under these conditions, it is imperative to develop a cure as soon as possible. On account of some of the adverse side effects of the existing conventional drugs, researchers all around the world are screening natural antiviral phytochemicals as potential therapeutic agents against COVID-19. This paper aims to review interactions of some specific phytochemicals with the receptor binding domain (RBD) of the Spike glycoprotein of SARS-CoV-2 and suggest their possible therapeutic applications. Literature search was done based on the wide array of in-silico studies conducted using broad spectrum phytochemicals against SARS-CoV-2 and other viruses. We shortlisted 26 such phytochemicals specifically targeting the S protein and its interactions with host receptors. To validate the previously published results, we also conducted molecular docking using the AutoDockVina application and identified 6 high potential phytochemicals for therapeutic use based on their binding energies. Besides this, availability of these compounds, their mode of action, toxicity data and cost-effectiveness were also taken into consideration. Our review specifically identifies 6 phytochemicals that can be used as potential treatments for COVID-19 based on their availability, toxicology results and low costs of production. However, all these compounds need to be further validated by wet lab experiments and should be approved for clinical use only after appropriate trials.

Download Full-text

In Silico Drug Discovery of 4-Hyroxypanduratin A, 6-Gingerol and Luteolin Targeting Nipah Virus

Journal of Pharmaceutical Research International ◽

10.9734/jpri/2021/v33i46b32964 ◽

2021 ◽

pp. 477-484

Author(s):

Anurag Verma ◽

Piyush Mittal ◽

Milind S. Pande ◽

Neelanchal Trivedi

Keyword(s):

Fusion Protein ◽

In Silico ◽

Virus Entry ◽

Nipah Virus ◽

Binding Energies ◽

Viral Agent ◽

In Silico Studies ◽

Viral Target ◽

Dietary Food

Nipah Virus is a zoo tonic virus and has re-emerged again with more deadliness. NiV has infected many animals and humans worldwide and a huge loss to life has been faced. NiV contains a Fusion protein on its outer membrane which helps in the virus entry into the host cell. This fusion protein is a virulent factor and is a major anti-viral target. Many medicinal plants have been used against viral diseases, current research aims towards the potential of three daily dietary food elements that can be used as an anti-viral agent. In-silico studies are performed with 4-hyroxypanduratin A, 6-gingerol and Luteolin against the NiV-F and binding energies were calculated. It was reported that these phyto-compounds have good negative binding energies and they have the promising potential against Nipah Virus. Further in-vitro research can be performed with these phyto-compounds to design a specific drug against Nipah Virus.

Download Full-text

In Silico Studies of Tumor Targeted Peptide-Conjugated Natural Products for Targeting Over-Expressed Receptors in Breast Cancer Cells Using Molecular Docking, Molecular Dynamics and MMGBSA Calculations

Applied Sciences ◽

10.3390/app12010515 ◽

2022 ◽

Vol 12 (1) ◽

pp. 515

Author(s):

Lucy R. Hart ◽

Charlotta G. Lebedenko ◽

Saige M. Mitchell ◽

Rachel E. Daso ◽

Ipsita A. Banerjee

Keyword(s):

Molecular Dynamics ◽

Molecular Docking ◽

In Silico ◽

Point Mutations ◽

Binding Energies ◽

Peptide Sequence ◽

Peroxisome Proliferator ◽

Peptide Conjugates ◽

Biological Studies ◽

In Silico Studies

In this work, in silico studies were carried out for the design of diterpene and polyphenol-peptide conjugates to potentially target over-expressed breast tumor cell receptors. Four point mutations were induced into the known tumor-targeting peptide sequence YHWYGYTPQN at positions 1, 2, 8 and 10, resulting in four mutated peptides. Each peptide was separately conjugated with either chlorogenate, carnosate, gallate, or rosmarinate given their known anti-tumor activities, creating dual targeting compounds. Molecular docking studies were conducted with the epidermal growth factor receptor (EGFR), to which the original peptide sequence is known to bind, as well as the estrogen receptor (ERα) and peroxisome proliferator-activated receptor (PPARα) using both Autodock Vina and FireDock. Based on docking results, peptide conjugates and peptides were selected and subjected to molecular dynamics simulations. MMGBSA calculations were used to further probe the binding energies. ADME studies revealed that the compounds were not CYP substrates, though most were Pgp substrates. Additionally, most of the peptides and conjugates showed MDCK permeability. Our results indicated that several of the peptide conjugates enhanced binding interactions with the receptors and resulted in stable receptor-ligand complexes; Furthermore, they may successfully target ERα and PPARα in addition to EGFR and may be further explored for synthesis and biological studies for therapeutic applications.

Download Full-text

In silico studies of bioactive compounds from selected African plants with inhibitory activity against nitric oxide synthase and arginase implicated in asthma

Egyptian Journal of Medical Human Genetics ◽

10.1186/s43042-021-00175-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Haruna Isiyaku Umar ◽

Tolulope Peter Saliu ◽

Sunday Solomon Josiah ◽

Adeola Ajayi ◽

Jamilu Bala Danjuma

Keyword(s):

Nitric Oxide ◽

Nitric Oxide Synthase ◽

Bioactive Compounds ◽

In Silico ◽

Active Sites ◽

Binding Energies ◽

Protein Database ◽

In Silico Studies ◽

Nos Inhibitors ◽

Oxide Synthase

Abstract Background It is a known fact that arginine is a common substrate for arginase and nitric oxide synthase (NOS). However, an imbalance between both enzymes could lead to a change in airway responses. Reports suggest that increased activities of both enzymes could lead to airway hyper-responsiveness. Thus, the requests for NOS inhibitors that can also inhibit arginase as the elevated activities of both enzymes have detrimental consequence on airways in asthma. Bioactive compounds from Azadirachta indica, Crinum glaucum, and Mangifera indica are documented for anti-inflammatory, immunomodulatory, anti-histaminic, smooth-muscle relaxants, and anti-allergic potentials. However, the mechanisms of action of these bioactive compounds in conferring the aforementioned protections are not well characterized. The objective of this present study is to assess in silico inhibitory potentials of these bioactive compounds against NOS and arginase via binding at their active sites. The crystal structures of NOS and arginase were retrieved from the protein database, while the bioactive compounds were retrieved from PubChem. Drug-likeness of the selected bioactive compounds was assessed using DruLiTo software. The successful compounds were docked with active sites of enzymes using AutoDock Vina docking software, and the docked complexes were analyzed using LigPlot and protein-ligand profiler web server. Results The findings of the study revealed that the bioactive compounds from A. indica, C. glaucum, and M. indica were able to interact with the active sites of NOS and arginase with the exception of gallic acid (from M. indica) and nimbandiol (from A. indica); these compounds showed differential binding energies (kcal/mol) and a number of them had higher binding energies than l-arginine when docked with NOS. Conclusion Conclusively, the in silico analysis proposes that these compounds could prove to be probable anti-asthmatic drugs.

Download Full-text

In-vitro anti-diabetic activity and in-silico studies of binding energies of palmatine with alpha-amylase, alpha-glucosidase and DPP-IV enzymes

Pharmacia ◽

10.3897/pharmacia.67.e58392 ◽

2020 ◽

Vol 67 (4) ◽

pp. 363-371

Author(s):

Patrick Okechukwu ◽

Mridula Sharma ◽

Wen Hui Tan ◽

Hor Kuan Chan ◽

Kavita Chirara ◽

...

Keyword(s):

In Silico ◽

Binding Energies ◽

Alpha Amylase ◽

Binding Interactions ◽

Inhibiting Effect ◽

Dpp Iv ◽

In Silico Studies ◽

Significant Difference ◽

Alpha Glucosidase

Palmatine a protoberberine alkaloid has been previously reported to possess in vivo antidiabetic and antioxidant property. The aim of the experiment is to evaluate the in vitro antidiabetic activity and in-silico studies of the binding energies of Palmatine, acarbose, and Sitagliptin with the three enzymes of alpha-amylase, alpha-glucosidase, and dipeptidyl peptidase-IV (DPP-IV). The in vitro antidiabetic study was done by evaluating the inhibitory effect of palmatine on the activities of alpha-amylase, alpha-glucosidase, and DPP-IV. Acarbose, and sitagliptin was used as standard drug. The molecular docking study was performed to study the binding interactions of palmatine with alpha-glucosidase, a-amylase, and DPP-IV. The binding interactions were compared with the standard compounds Sitagliptin and acarbose. Palmatine with IC50 (1.31 ± 0.27 µM) showed significant difference of (< 0.0001) higher inhibiting effect on alpha-amylase and weak inhibiting effect on alpha-glucosidase enzyme with IC50 (9.39 ± 0.27 µM) and DPP-IV with IC50 (8.7 ± 1.82 µM). Palmatine possess inhibition effect on the three enzymes.

Download Full-text

Natural compounds as potential inhibitors of novel coronavirus (COVID-19) main protease: An in silico study

10.21203/rs.3.rs-22839/v1 ◽

2020 ◽

Cited By ~ 3

Author(s):

Amaresh Mishra ◽

Yamini Pathak ◽

Vishwas Tripathi

Keyword(s):

In Silico ◽

Structural Diversity ◽

Natural Compounds ◽

Binding Energies ◽

Maslinic Acid ◽

Main Protease ◽

In Silico Studies ◽

Gallocatechin Gallate ◽

Novel Coronavirus ◽

Potential Inhibitors

Abstract COVID-19 pandemic, a novel coronavirus disease is caused by severe acute respiratory syndrome corona virus, SARS-CoV-2. It was first reported in Wuhan, China and has now expanded to more than 190 countries across the world. Till date, there is no specific medication available to prevent or target SARS CoV-2 infection. Very recently, the crystal structure of COVID- 19 main protease (Mpro) was revealed by Liu et al. (2020). SARS-CoV-2 main protease (Mpro) is a key enzyme that plays a crucial role in viral replication and transcription. Thus, Mpro could be a promising target to inhibit SARS-CoV-2 infection. Natural compounds due to their structural diversity and safety are considered as an excellent source of antiviral drugs. In this study, we selected Herbacetin, Rhoifolin, Pectolinarin, Apigenin, Luteolin, Amentoflavone, Daidzein, Puerarin, Epigallocatechin, Gallocatechin gallate, Resveratrol, Maslinic acid, Piperine and Ganomycin B to target the SARS-CoV-2 main protease (Mpro) using in silico tools. These compounds were examined based on ADME, drug likeness, docking studies, MD simulations using CABS-flex 2.0, and prediction of major toxicity parameters (hepatotoxicity & cytotoxicity) to check the safety aspects of the selected compounds. We also investigated the similarity of these compounds, if any, with FDA approved drugs using Swiss similarity. The docking results were found in the order of Amentoflavone (-9.13 kcal/mol), Ritonavir (-8.52 kcal/mol), Lopinavir (-8.5 kcal/mol), Puerarin (-7.97 kcal/mol), Maslinic acid (-7.97 kcal/mol), Piperine (-7.65 kcal/mol), Gallocatechin gallate (-7.59 kcal/mol), Luteolin (-7.58 kcal/mol), Apigenin (-7.42 kcal/mol), Resveratrol (-7.41 kcal/mol), Herbacetin (-7.4 kcal/mol), Daidzein (-7.32 kcal/mol), Rhoifolin (-6.71 kcal/mol), Ganomycin B (-6.46 kcal/mol), Epigallocatechin (-6.13 kcal/mol), and Pectolinarin (-5.88 kcal/mol). Among these selected natural compounds, Amentoflavone and Puerarin were the two top leads which showed the lowest binding energies. Interestingly, Amentoflavone showed highest binding affinity among all the selected compounds. Our promising findings based on in-silico studies warrants further clinical trial in order to use these compounds as potential inhibitors of SARS-CoV-2 protease.

Download Full-text

Zingiber officinale: Ayurvedic Uses of the Plant and In Silico Binding Studies of Selected Phytochemicals With Mpro of SARS-CoV-2

Natural Product Communications ◽

10.1177/1934578x211031766 ◽

2021 ◽

Vol 16 (10) ◽

pp. 1934578X2110317

Author(s):

Rownak Jahan ◽

Alok K. Paul ◽

Tohmina A. Bondhon ◽

Anamul Hasan ◽

Khoshnur Jannat ◽

...

Keyword(s):

Chlorogenic Acid ◽

In Silico ◽

Three Dimensional ◽

Zingiber Officinale ◽

Binding Energies ◽

Binding Affinities ◽

Binding Studies ◽

High Binding ◽

Main Protease ◽

In Silico Studies

Among the large number of plants that are part of the Ayurvedic system of medicine in India and Bangladesh, Zingiber officinale Roscoe (Zingiberaceae), or ginger in English, holds a special place and is often referred to as “Mahaushadha” (great medicine) and “Vishvabhesaja” (worldwide or universal herb) to signify its special status. The plant and particularly its rhizomes are used both in the raw and dry form for the relief of a multitude of disorders. Since a number of these disorders occur in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it was of interest to perform in silico studies (molecular docking) to evaluate the binding affinities of a number of constituents of Zingiber officinale with the 3C-like protease or main protease (Mpro) of SARS-CoV-2, which plays an essential role in the cleavage of viral polyproteins and subsequent viral replication. Our studies indicated that 2 of the compounds present in ginger, namely, chlorogenic acid and hesperidin, had high binding affinities for Mpro with predicted binding energies of −7.5 and −8.3 kcal/mol. The two-dimensional and three-dimensional interactions also showed that, while chlorogenic acid interacts with one of the His41 amino acids of the catalytic dyad of Mpro, hesperidin interacts with the other amino acid Cys145, which can account for their predicted high binding energies and, therefore, possibly can inhibit Mpro activity. Taken together, our findings indicate that ginger, besides alleviating the symptoms induced by SARS-CoV-2, may also play a role in inhibiting the virus.

Download Full-text

In Silico Investigation on the Interaction of Chiral Phytochemicals from Opuntia ficus-indica with SARS-CoV-2 Mpro

Symmetry ◽

10.3390/sym13061041 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1041

Author(s):

Caterina Vicidomini ◽

Valentina Roviello ◽

Giovanni N. Roviello

Keyword(s):

In Silico ◽

Quinic Acid ◽

Antiviral Drugs ◽

Binding Energies ◽

Binding Affinities ◽

Opuntia Ficus Indica ◽

Web Based ◽

Protein Targets ◽

Main Protease ◽

In Silico Studies

Opuntia ficus-indica is a cactaceous plant native to America but, nowadays, widely found worldwide, having been the most common domesticated species of cactus grown as a crop plant in semiarid and arid parts of the globe, including several Mediterranean basin countries. Opuntia ficus-indica can be regarded as a medicinal plant, being source of numerous bioactive phytochemicals such as vitamins, polyphenols, and amino acids. The urgent need for therapeutic treatments for the COronaVIrus Disease 19 (COVID-19), caused by the Severe Acute Respiratory Syndrome (SARS)-Coronavirus (CoV)-2, justifies the great attention currently being paid not only to repurposed antiviral drugs, but also to natural products and herbal medications. In this context, the anti-COVID-19 utility of Opuntia ficus-indica as source of potential antiviral drugs was investigated in this work on the basis of the activity of some of its phytochemical constituents. The antiviral potential was evaluated in silico in docking experiments with Mpro, i.e., the main protease of SARS-CoV-2, that is one of the most investigated protein targets of therapeutic strategies for COVID-19. By using two web-based molecular docking programs (1-Click Mcule and COVID-19 Docking Server), we found, for several flavonols and flavonol glucosides isolated from Opuntia ficus-indica, good binding affinities for Mpro, and in particular, binding energies lower than −7.0 kcal/mol were predicted for astragalin, isorhamnetin, isorhamnetin 3-O-glucoside, 3-O-caffeoyl quinic acid, and quercetin 5,4′-dimethyl ether. Among these compounds, the chiral compound astragalin showed in our in silico studies the highest affinity for Mpro (−8.7 kcal/mol) and also a low toxicity profile, emerging, thus, as an interesting protease inhibitor candidate for anti-COVID-19 strategies.

Download Full-text

In vitro and in silico studies of two 1,4-naphthoquinones and their topical formulation in bigels

Current Drug Delivery ◽

10.2174/1567201818666210618111118 ◽

2021 ◽

Vol 18 ◽

Author(s):

Imen Khelifi ◽

Audrey Tourrette ◽

Daycem Khelifi ◽

Thomas Efferth ◽

El Akrem Hayouni ◽

...

Keyword(s):

Molecular Docking ◽

In Silico ◽

Water Solubility ◽

Biological Activities ◽

Binding Energies ◽

Topical Formulation ◽

Plant Metabolites ◽

Secondary Plant Metabolites ◽

In Silico Studies

Background: 1,4-Naphthoquinones (1,4-NQs) are secondary plant metabolites with numerous biological activities. 1,4-NQs display low water solubility and poor bioavailability. Bigels are a new technology with great potential, which are designated as drug delivery systems. Biphasic bigels consisting of solid and liquid components represent suitable formulations improving the diffusion and bioavailability of NQs into the skin. Objective: We evaluated the in silico and in vitro activity of 5,8-dihydroxy-1,4-naphthoquinone (M1) and 2,3-dichloro-5,8-dihydroxy-1,4-naphthoquinone (M2) on elastase and assessed their cytotoxicity towards COLO38 melanoma cells. The 1,4-NQs were loaded into bigels for topical application. Methods: Molecular docking was performed, and cytotoxicity was evaluated on COLO38 cells using the resazurin assay. M1 and M2 were separately incorporated into bigels consisting of hydrogel organogel with sweet almond oil as a non-polar solvent and span 65 as organogelator. Their rheological behavior and microscopic properties were characterized. The diffusion kinetics and permeation of 1,4-NQs from bigels were studied by a paddle-over-extraction cell and a “Franz cell” in vitro permeation model. Results: Molecular docking data predicted high interactions between elastase and ligands. Hydrogen bonds to LYS233 were observed for M1, M2, and phosphoramidon (positive control). The average binding energies were -8.5 and -9.7 kcal/mol for M1 and M2 and -12.6 kcal/mol for phosphoramidon. M1 and M2 inhibited the elastase activity by 58.9 and 56.6%, respectively. M1 and M2 were cytotoxic towards COLO38 cells (IC50: 2.6 and 9.8 µM) y. The M1 release from bigels was faster and more efficient than that of M2. Conclusion: M1 and M2 are promising for skin disease treatment. Biphasic organogel-hydrogel bigels are efficient and safe formulations to overcome their low bioavailability.

Download Full-text

Synthesis of novel ketene dithioacetals via one pot reaction: Molecular modelling in-silico Admet studies and antimicrobial activity

Current Chemistry Letters ◽

10.5267/j.ccl.2021.1.003 ◽

2021 ◽

pp. 187-202

Author(s):

Mohammad Arif Pasha ◽

Sumanta Mondal ◽

Naresh Panigrahi

Keyword(s):

In Silico ◽

Binding Energies ◽

Inhibition Mechanism ◽

Good Prediction ◽

One Pot ◽

Ketene Dithioacetals ◽

In Silico Admet ◽

In Silico Studies ◽

Three Component Reaction

A simple and efficient method for the synthesis of fifteen novel ketene dithioacetals (2-(6-amino5-cyano-4-aryl-4H-1,3-dithiin-2-ylidene) malononitrile) via a one-pot three-component reaction of activated methylene group malononitrile with carbon disulfide in the presence of arylidene malononitriles were reported. The effects of LiOH.H2O as a base at different concentrations have been investigated and can provide products in good yields at 40-50ºC temperature (54-89%). All the synthesized ketene dithioacetals compounds (MCB1-MCB15) were checked for favorable pharmacokinetic param¬eters along with toxicities which are based on drug-likeness explained by Lipinski’s rule of five by Med chem designer software correlated with that of pkCSM online tool. Explorations of synthesized ketene dithioacetals compounds for the antimicrobial study were found to be effective towards Staphylococcus aureus (MCB5 and MCB13) with a zone of inhibition at 26mm and 22mm which is compared to that of standard ciprofloxacin (26mm). This made our study to explore the inhibition mechanism with the help of molecular docking studies with possible binding energies (-6.4 to -8.9 kJ/mol) by pyrx 0.8 software to represent a good prediction of interactions between the ligand and protein (2XCT). Further evaluation of druggability and ADMET predictions compounds MCB5 and MCB13 were found to be effective. Based on the in-vitro and in-silico studies a series of ketene dithioacetals compounds may be helpful for further studying SAR and designing more potent antimicrobials.

Download Full-text