Molecular Docking Study on the Interaction of Riboflavin (Vitamin B2) and Cyanocobalamin (Vitamin B12) Coenzymes

Cobalamins are the largest and structurally complex cofactors found in biological systems and have attracted considerable attention due to their participation in the metabolic reactions taking place in humans, animals, and microorganisms. Riboflavin (vitamin B2) is a micronutrient and is the precursor of coenzymes, FMN and FAD, required for a wide variety of cellular processes with a key role in energy-based metabolic reactions. As coenzymes of both vitamins are the part of enzyme systems, the possibility of their mutual interaction in the body cannot be overruled. A molecular docking study was conducted on riboflavin molecule with B12 coenzymes present in the enzymes glutamate mutase, diol dehydratase, and methionine synthase by using ArgusLab 4.0.1 software to understand the possible mode of interaction between these vitamins. The results from ArgusLab showed the best binding affinity of riboflavin with the enzyme glutamate mutase for which the calculated least binding energy has been found to be −7.13 kcal/mol. The results indicate a significant inhibitory effect of riboflavin on the catalysis of B12-dependent enzymes. This information can be utilized to design potent therapeutic drugs having structural similarity to that of riboflavin.

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Molecular Docking Study for Analyzing the Inhibitory Effect of Anti-inflammatory Plant Compound Against Tumour Necrosis Factor (TNF-α)

Current Drug Therapy ◽

10.2174/1574885513666180503145352 ◽

2019 ◽

Vol 14 (1) ◽

pp. 85-90

Author(s):

Sagarika Biswas

Keyword(s):

Molecular Docking ◽

Tumour Necrosis Factor ◽

Tumour Necrosis ◽

Docking Study ◽

Developed Countries ◽

Inhibitory Effect ◽

Molecular Docking Study ◽

Drug Designing ◽

Anti Inflammatory ◽

Necrosis Factor

Background: Rheumatoid Arthritis (RA) is an autoimmune disorder of symmetric synovial joints which is characterized by the chronic inflammation with 0.5-1% prevalence in developed countries. Presence of persistent inflammation is attributed to the major contribution of key inflammatory cytokine and tumour necrosis factor- alpha (TNF- α). Recent drug designing studies are developing TNF-α blockers to provide relief from the symptoms of the disease such as pain and inflammation. Available blockers are showing certain limitations such as it may enhance the rate of tuberculosis (TB) occurrence, lymphoma risk, cost issues and certain infections are major concern. Discussed limitations implicated a need of development of some alternative drugs which exhibit fewer side effects with low cost. Therefore, we have identified anti-inflammatory compounds in an underutilized fruit of Baccaurea sapida (B.sapida) in our previous studies. Among them quercetin have been identified as the most potent lead compound for drug designing studies of RA. Methods: In the present article, characterization of quercetin has been carried out to check its drug likeliness and molecular docking study has been carried out between TNF- α and quercetin by using AutoDock 4.2.1 software. Further, inhibitory effect of B. sapida fruit extract on RA plasma has been analysed through immunological assay ELISA. Results: Our in-silico analysis indicated that quercetin showed non carcinogenic reaction in animal model and it may also cross the membrane barrier easily. We have studied the ten different binding poses and best binding pose of TNF-α and quercetin showed -6.3 kcal/mol minimum binding energy and 23.94 µM inhibitory constant. In addition to this, ELISA indicated 2.2 down regulated expression of TNF-α in RA compared to control. Conclusion: This study may further be utilized for the drug designing studies to reduce TNF-α mediated inflammation in near future. This attempt may also enhance the utilization of this plant worldwide.

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Studi Penambatan Molekul Senyawa Curcuma longa pada Bakteri Resisten Carbapenem Acinetobacter baumanii dengan Metode In Silico

Jurnal Integrasi Kesehatan & Sains ◽

10.29313/jiks.v3i1.7417 ◽

2021 ◽

Vol 3 (1) ◽

pp. 124-130

Author(s):

Nabila Shafa Athharani ◽

Nugraha Sutadipura ◽

Yuli Susanti

Keyword(s):

Molecular Docking ◽

In Silico ◽

Raw Materials ◽

Curcuma Longa ◽

Docking Study ◽

The Body ◽

Molecular Docking Study ◽

Acinetobacter Baumanii ◽

Docking Method

Penemuan berbagai senyawa obat baru dari berbagai proses penelitian yang semakin memperjelas peran penting studi komputasi sebagai dasar awal untuk menemukan sumber bahan baku obat baik dari alam maupun sintetis. Infeksi nosokomial dapat disebabkan oleh bakteri, virus atau patogen lain di rumah sakit, dan ditularkan melalui peralatan di rumah sakit. Salah satu bakteri yang paling sering menyebabkan infeksi adalah Acinetobacter baumanii bakteri tersebut dapat membangun resistensi dalam tubuh. Metode penelitian ini dilakukan secara in silico dengan metode molecular docking dengan melihat penambatan molekul senyawa yang dimilikinya. Hasil penelitian menunjukkan bahwa senyawa yang diuji terhadap target reseptor yaitu Acinetobacter baumanii memiliki kemampuan sebagai antibakteri, terlihat dari ikatan afinitas yang diperoleh dari sekitar -7,7 kkal/mol hingga -8,1 kkal/mol. Kesimpulannya, kunyit dapat digunakan sebagai kandidat untuk mencegah Acinetobacter baumanii menjadi resisten. Molecular Docking Study of Curcuma Longa Compounds on Bacteria Resistant Carbapenem Acinetobacter Baumanii with in Silico MethodThe discovery of various new medicinal compounds from various research processes that further clarify the important role of computational studies as the initial basis for finding sources of medicinal raw materials both from natural and synthetic. Nosocomial infections can be caused by bacteria, viruses or other pathogens in the hospital and transmitted through equipment in the hospital. One of the bacteria that most often causes infection is Acinetobacter baumanii where these bacteria can build up resistance in the body. Method of this research is carried out in silico with the molecular docking method by looking at the docking of its compound molecules. The results showed that of the compounds tested against the receptor target, Acinetobacter Baumanii, had the ability as antibacterial, seen from the affinity bonds obtained from around -7.7 kcal/mol to -8.1 kcal/mol. Conclusion is turmeric can be used as a candidate to prevent Acinetobacter baumanii from becoming resistance.

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Thymoquinone: A Review of Pharmacological Importance, Oxidative Stress, COVID-19, and Radiotherapy

Mini-Reviews in Medicinal Chemistry ◽

10.2174/1389557522666220104151225 ◽

2022 ◽

Vol 22 ◽

Author(s):

Seyithan Taysi ◽

Firas Shawqi Algburi ◽

Zaid Mohammed ◽

Omeed Akbar Ali ◽

Muhammed Enes Taysi

Keyword(s):

Molecular Docking ◽

Alternative Medicine ◽

Nigella Sativa ◽

Serine Proteinase ◽

Receptor Site ◽

Docking Study ◽

Inhibitory Effect ◽

Docking Studies ◽

Molecular Docking Study ◽

Main Component

Widely consumed worldwide, Nigella sativa (NS) is a medicinal herb commonly used in various alternative medicine systems such as Unani and Tibb, Ayurveda, and Siddha. Recommended for regular use in Tibb-e-Nabwi (Prophetic Medicine), NS is considered one of the most notable forms of healing medicine in Islamic literature. Thymoquinone (TQ), the main component of the essential oil of NS, has been reported to have many properties such as antioxidant, anti-inflammatory, antiviral, and antineoplastic. Its chemical structure indicates antiviral potential against many viruses, including the hepatitis C virus, human immunodeficiency virus, and other coronavirus diseases. Interestingly, molecular docking studies have demonstrated that TQ can potentially inhibit the development of the coronavirus disease 2019 (COVID-19) by binding to the receptor site on the transmembrane serine proteinase 2 (the activator enzyme that attaches the virus to the cell). In addition, TQ has been shown to be effective against cancer cells due to its inhibitory effect by binding to the different regions of MDM2, according to the proposed molecular docking study. Detailed in this review is the origin of TQ, its significance in alternative medicine, pharmacological value, potential as a cancer anti-proliferative agent, use against the coronavirus disease 2019 (COVID-19), and treatment of other diseases.

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Divergent de novo synthesis of 2,4,5-trideoxyhexopyranosides derivatives of podophyllotoxin as anticancer agents

Future Medicinal Chemistry ◽

10.4155/fmc-2018-0593 ◽

2019 ◽

Vol 11 (23) ◽

pp. 3015-3027 ◽

Cited By ~ 2

Author(s):

Yapeng Lu ◽

Lu Wang ◽

Xinyang Wang ◽

Haoliang Yuan ◽

Yu Zhao

Keyword(s):

Molecular Docking ◽

Anticancer Agents ◽

De Novo ◽

Docking Study ◽

Inhibitory Effect ◽

De Novo Synthesis ◽

Molecular Docking Study ◽

Cytotoxicity Activity ◽

Derivatives Of ◽

Mcf 7

Aim: Identification of new anticancer glycosidic derivatives of podophyllotoxin. Methods: 14 podophyllotoxin D- and L-monosaccharides have been synthesized in three steps employing de novo glycosylation strategy, and their abilities to inhibit the growth of HeLa, HepG2, MCF-7, A549 and MDA-MB-231 cancer cells were investigated by MTT assay. Molecular docking study of compound 5j with tubulin was performed. Immunofluorescence was applied for detecting the inhibitory effect of 5j on tubulin polymerization. Results & conclusion: Most of synthesized compounds showed strong cytotoxicity activity against five cancer cell lines. Compound 5j possessed the highest cytotoxicity with the IC50 values from 41.6 to 95.2 nM, and could concentration-dependently inhibit polymerization of the microtubule cytoskeleton of MCF-7 cells. Molecular docking disclosed that sugar moiety-dedicated hydrogen bond endowed 5j a higher binding affinity for tubulin.

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In vitro MAO-B Inhibitory Effect of Citrus trifoliata L. via Enzyme Assay and Molecular Docking Study

Egyptian Journal of Chemistry ◽

10.21608/ejchem.2019.14735.1892 ◽

2019 ◽

Vol 0 (0) ◽

pp. 0-0

Author(s):

Mostafa Abd El Kawy ◽

Camilia Michel ◽

Farid Kirollos ◽

Ahmed El Kerdawy ◽

Mohamed sedeek

Keyword(s):

Molecular Docking ◽

Enzyme Assay ◽

Docking Study ◽

Inhibitory Effect ◽

Molecular Docking Study ◽

Mao B

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Molecular docking study on columbin isolated from Tinospora cordifolia as a cholinesterase inhibitor

Tropical Journal of Pharmaceutical Research ◽

10.4314/tjpr.v20i2.17 ◽

2022 ◽

Vol 20 (2) ◽

pp. 337-343

Author(s):

Joel O. Onoja ◽

Taiwo O. Elufioye ◽

Zaid A. Sherwani ◽

Zaheer Ul-Haq

Keyword(s):

Molecular Docking ◽

Goodness Of Fit ◽

Colorimetric Assay ◽

Structure Refinement ◽

Ethyl Acetate Fraction ◽

Docking Study ◽

Inhibitory Effect ◽

Tinospora Cordifolia ◽

Molecular Docking Study

Purpose: To investigate the acetylcholinesterase (AChE) inhibitory potential of columbin and also to assess its binding affinity against AChE protein. Methods: Crystals of columbin were isolated from the ethyl acetate fraction of Tinospora cordifolia using column chromatography and its structure was determined using x-ray crystallography. Ellman colorimetric assay was used to determine the AChE inhibitory effect in vitro while molecular docking was performed using the MOE 2015.010 software. The selected protein data bank (PDB) was modeled using PDB ID: 10CE (pacific electric ray). Results: The crystal and structure refinement data of columbin were: C20H22O6, Orthorhombic, P212121, a = 7.4951(2) Å (α = 90°), b = 11.6451(3) Å (β = 90°), c = 19.5882(5) Å (γ = 90°), V=1709.68(8) Å3, Z = 4, Density (calculated) = 1.392 Mg/m3, absorption coefficient = 0.851 mm-1, goodness-of-fit on F2 =1.091, T = 100(2) K. Columbin demonstrated good AChE inhibitory effect with half-maximal inhibitory concentration (IC50) of 1.2993 ± 0.17 mg/mL. Molecular docking data revealed that it exhibited hydrophobic and hydrogen bonding interactions with the surrounding residues, and this accelerated complexation between the ligands and the active site of the enzyme. Conclusion: Columbin may be useful in the management of neurodegenerative conditions such as Alzheimer’s disease.

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Antioxidant and Antiproliferative Potential of Bioactive Molecules Ursolic Acid and Thujone Isolated from Memecylon edule and Elaeagnus indica and Their Inhibitory Effect on Topoisomerase II by Molecular Docking Approach

BioMed Research International ◽

10.1155/2020/8716927 ◽

2020 ◽

Vol 2020 ◽

pp. 1-12 ◽

Cited By ~ 1

Author(s):

Ramalingam Srinivasan ◽

Arumugam Aruna ◽

Jong Suk Lee ◽

Myunghee Kim ◽

Muthugounder Subramaniam Shivakumar ◽

...

Keyword(s):

Molecular Docking ◽

Ursolic Acid ◽

Topoisomerase Ii ◽

Docking Study ◽

Inhibitory Effect ◽

Significant Inhibition ◽

Bioactive Molecules ◽

Molecular Docking Study ◽

Docking Approach ◽

Free Radicals Scavenging

The present study aimed to evaluate the antioxidant and antiproliferative potential of ursolic acid and thujone isolated from leaves of Elaeagnus indica and Memecylon edule and their inhibitory effect on topoisomerase II using molecular docking study. The isolated ursolic acid and thujone were examined for different types of free radicals scavenging activity, the antiproliferative potential on U-937 and HT-60 cell lines by adopting standard methods. Further, these compounds were docked with the active site of the ATPase region of topoisomerase II. The findings of the research revealed that ursolic acid harbor strong antioxidant and antiproliferative capacity with low IC50 values than the thujone in all tested methods. Moreover, ursolic acid shows significant inhibition effect on topoisomerase II with a considerable docking score (−8.0312) and GLIDE energy (−51.86 kca/mol). The present outcome concludes that ursolic acid possesses significant antioxidant and antiproliferative potential, which can be used in the development of novel antioxidant and antiproliferative agents in the future.

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Binding Properties of Photosynthetic Herbicides with the QB Site of the D1 Protein in Plant Photosystem II: A Combined Functional and Molecular Docking Study

Plants ◽

10.3390/plants10081501 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1501

Author(s):

Beatrice Battaglino ◽

Alessandro Grinzato ◽

Cristina Pagliano

Keyword(s):

Molecular Docking ◽

Photosystem Ii ◽

D1 Protein ◽

Photosynthetic Electron Transport ◽

Docking Study ◽

Inhibitory Effect ◽

Thylakoid Membranes ◽

Binding Affinities ◽

Molecular Docking Study ◽

Future Design

Photosystem II (PSII) is a multi-subunit enzymatic complex embedded in the thylakoid membranes responsible for the primary photosynthetic reactions vital for plants. Many herbicides used for weed control inhibit PSII by interfering with the photosynthetic electron transport at the level of the D1 protein, through competition with the native plastoquinone for the QB site. Molecular details of the interaction of these herbicides in the D1 QB site remain to be elucidated in plants. Here, we investigated the inhibitory effect on plant PSII of the PSII-inhibiting herbicides diuron, metobromuron, bentazon, terbuthylazine and metribuzin. We combined analysis of OJIP chlorophyll fluorescence kinetics and PSII activity assays performed on thylakoid membranes isolated from pea plants with molecular docking using the high-resolution PSII structure recently solved from the same plant. Both approaches showed for terbuthylazine, metribuzin and diuron the highest affinity for the D1 QB site, with the latter two molecules forming hydrogen bonds with His215. Conversely, they revealed for bentazon the lowest PSII inhibitory effect accompanied by a general lack of specificity for the QB site and for metobromuron an intermediate behavior. These results represent valuable information for future design of more selective herbicides with enhanced QB binding affinities to be effective in reduced amounts.

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Hispidin and Lepidine E: two Natural Compounds and Folic acid as Potential Inhibitors of 2019-novel coronavirus Main Protease (2019-nCoVMpro), molecular docking and SAR study

Current Computer - Aided Drug Design ◽

10.2174/1573409916666200422075440 ◽

2020 ◽

Vol 16 ◽

Cited By ~ 9

Author(s):

Talia Serseg ◽

Khedidja Benarous ◽

Mohamed Yousfi

Keyword(s):

Molecular Docking ◽

Folic Acid ◽

Docking Study ◽

Natural Compounds ◽

Inhibitory Effect ◽

World Health ◽

Molecular Docking Study ◽

Main Protease ◽

Novel Coronavirus ◽

Health Organization

: 2019-nCoVis a novel coronavirus was isolated and identified in 2019 in Wuhan, China. On 17 February and according to the world health organization, a number of 71 429 confirmed cases worldwide, among them 2162 new cases recorded in the last 24 hours. One month later the confirmed cases jumped to 179111, with 11525new cases in the last 24 hours, with 7426total deaths. There is no drug or vaccine for humanand animal coronavirus.The inhibition of 3CL hydrolase enzyme provides a promising therapeutic principle for developing treatments against CoViD-19.The 3CLpro (Mpro) known for involving in counteracting the host innate immune response.Thiswork presents the inhibitory effect of some natural compounds against 3CL hydrolase enzyme, and explain the main interactions in inhibitor-enzyme complex. Molecular docking study carried out using Autodock Vina. By screening several molecules, we identified three candidate agents that inhibit the main protease of coronavirus. Hispidin, lepidine E,and folic acid bound tightly in the enzyme, strong hydrogen bonds have been formed (1.69-1.80Å) with the active site residues.This study provides a possible therapeutic strategy for CoViD-19.

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