Molecular docking based screening dynamics for plant based identified potential compounds of PDE12 inhibitors

Nirmalraj, Selvaraj; Gayathiri, Ekambaram; Sivamurugan, Malathi; Manivasagaperumal, R.; Jayanthi, J.; Prakash, Palanisamy; Selvam, Kuppusamy

doi:10.1016/j.crgsc.2021.100122

Cited by 8 publications

(3 citation statements)

References 12 publications

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“…β-sesquiphellandrene was also one of the primary sesquiterpenes contributing to the antioxidant activity of Curcuma species (Zhao et al, 2010). Moreover, the ability to scavenge free radicals of DC-HX might come from other significant phytoconstituents, such as nhexadecanoic acid (Kalpana Devi V et al, 2012) or trans-13-octadecenoic acid (Selvaraj et al, 2021), but also from minor compounds with intense antioxidant activity, such as β-bisabolene (Kazemi and Rostami, 2015), caryophyllene oxide (Karakaya et al, 2020) or dodecanoic acid (lauric acid) (Henry et al, 2002).…”

Section: Volatile Components Analysismentioning

confidence: 99%

“…These compounds were reported in the Distichochlamys species for the first time. They also exhibited various pharmacological effects such as the anti-inflammatory property (Aparna et al, 2012) and the anticancer potential (Bharath et al, 2021) for n-hexadecanoic acid; the antiviral activity of trans-13-octadecenoic acid (Selvaraj et al, 2021); the antimicrobial activity (Ceyhan-Güvensen and Keskin, 2016) and the antiinflammatory effect (Bhardwaj et al, 2020) for neophytadiene.…”

Section: Volatile Components Analysismentioning

confidence: 99%

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Antioxidant and antithrombotic activities of the Distichochlamys citrea leaves extract

Nguyen,

Nguyen Thi,

Nguyen

et al. 2023

Vietnam J. Biotechnol.

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Distichochlamys citrea (DC) is an endemic ginger species used in treating associated-heart diseases in traditional medicine in Vietnam. However, scientific evidence to support the local use of this plant was limited. The present study aimed to investigate the antioxidant and antithrombotic activities of D. citrea extracts for the first time. The antioxidant activity of DC extracts was assessed by scavenging DPPH radical and measuring their total phenolic content (TPC). The antithrombotic activity was evaluated by inhibiting platelet aggregation and prolonging blood coagulation. Volatile components elucidated by GC-MS were docked with typical platelet receptors, including COX-1 and P2Y12. Results showed that the methanol extract of D. citrea exhibited a stronger DPPH scavenging ability (IC50 = 0.33 ± 0.00 mg/mL) and a higher TPC (8.09 ± 0.21%) than other extracts (p < 0.05). On the other hand, the hexane extract of D. citrea (DC-HX) had a remarkable inhibiting impact on ADP-, collagen- and ristocetin–induced platelet aggregation in a dose-dependent manner (Pearson’s correlation, r > 0.90, p < 0.05). In contrast, this extract did not lengthen the clotting time through any factors, such as PT (prothrombin time), and TT (thrombin time), except for APTT (activated partial thromboplastin time) at 4 mg/mL of the extract. GC-MS revealed that oxygenated hydrocarbons (54.45%) dominated the volatile profile of DC-HX, followed by sesquiterpens (37.18%) and diterpenes (6.66%). In the platelet aggregation process, several compounds in DC-HX were firmly bound to COX-1 and P2Y12, which might partly explain the significant antiaggregatory activity of this fraction. In conclusion, Distichochlamys citrea may be a potential source of active phytoconstituents for treating radicals- and cardiovascular-associated diseases.

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Section: Volatile Components Analysismentioning

confidence: 99%

Section: Volatile Components Analysismentioning

confidence: 99%

Antioxidant and antithrombotic activities of the Distichochlamys citrea leaves extract

Nguyen,

Nguyen Thi,

Nguyen

et al. 2023

Vietnam J. Biotechnol.

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“…The molecular docking tool is used to study the inclination of small drug molecule with the protein target to predict its binding affinity and interactions. The tool plays a major role in the ethical design of medicines and is also involved in modern advanced drug testing [ 10 ]. The technique predicts the toxicity effects of the compounds.…”

Section: Introductionmentioning

confidence: 99%

Hecogenin a Plant Derived Small Molecule as an Antagonist to BACE-1: A Potential Target for Neurodegenerative Disorders

et al. 2023

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The field of drug discovery has recognized the significance of computer-aided drug design. Recent advancements in structure identification and characterization, bio-computational science and molecular biology have significantly contributed to the development of novel treatments for various diseases. Alzheimer’s disease is prevalent in over 50 million affected people, with the pathological condition of amyloidal plaque formation by the beta-amyloidal peptide that results in lesions of the patient’s brain, thus making the target prediction and treatment a hurdle. In this study, we evaluated the potential of 54 bioactive compounds from Justicia adhatoda L. and Sida cordifolia L. identified through LC-MS/MS against the β-site amyloid precursor cleaving enzyme (beta-secretase) that results in the formation of amyloidal plaques. To study the drug-likeness of the phytocompounds, Lipinski’s rule of five for ADME profiling and toxicity prediction was performed. Molecular docking was performed using auto-dock tool of PyRx software; molecular dynamic simulations were performed using the Schrodinger suite. Molecular docking against BACE-1 protein revealed that hecogenin, identified from S. cordifolia has a broad spectrum of pharmacological applications and a binding affinity score of −11.3 kcal/Mol. The Hecogenin–BACE-1 protein complex was found to be stable after 30 ns of MD simulation, resulting in its substantial stability. Further studies focusing on the in vivo neuroprotective activity of hecogenin against the disease will pave the way for efficient drug discovery from natural sources in a precise manner.

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Machine learning-integrated and fingerprint-based similarity search against immuno oncology library for identification of novel ERK2 inhibitors

Suryawanshi,

Pawar,

Kolpe

et al. 2024

Struct Chem

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Molecular docking based screening dynamics for plant based identified potential compounds of PDE12 inhibitors

Cited by 8 publications

References 12 publications

Antioxidant and antithrombotic activities of the Distichochlamys citrea leaves extract

Antioxidant and antithrombotic activities of the Distichochlamys citrea leaves extract

Hecogenin a Plant Derived Small Molecule as an Antagonist to BACE-1: A Potential Target for Neurodegenerative Disorders

Machine learning-integrated and fingerprint-based similarity search against immuno oncology library for identification of novel ERK2 inhibitors

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