Molecular Docking Analysis: Interaction Studies of Natural Compounds to Anti-inflammatory Targets

Abstract

A variety of compounds from medicinal plants have been reported to possess antiinflammatory properties. Selected natural compounds that exhibit anti-inflammatory properties were subjected to docking simulation using AutoDock Vina to investigate their interaction modes to the potential macromolecular targets. The docking was performed using different molecular targets, i.e., cyclooxygenase-2, phospholipase A2, NF-κB inhibitor, and interleukin-1 receptor. It revealed that flavonoids have the highest affinity to the macromolecular targets (the lowest binding energy values) and the highest consistency of interaction model. Some terpenoids were identified to have potential inhibitor of phospholipase A2.

Anti-Inflammatory and Anti-Rheumatic Potential of Selective Plant Compounds by Targeting TLR-4/AP-1 Signaling: A Comprehensive Molecular Docking and Simulation Approaches

“…), the selected compounds showed considerable anti-inflammatory activity and marked improvement in the underlying inflammatory activities. These compounds, on the other hand, were not tested for anti-arthritic activity against TLR-4 and downstream signaling proteins such as MAPKs (JNK), AP-1 (activation protein-1), and NF-κB [19,20]. TLR-4 signaling plays a key role in arthritis pathogenesis by activating a number of downstream signaling proteins including MAPKs (JNK), AP-1, and NF-κB.…”

“…Furthermore, despite their different biological functions, the pharmacokinetic and toxicokinetic aspects of these drugs have not been thoroughly investigated. Any compound's pharmacokinetic and toxicokinetic properties have a substantial impact on its pharmacodynamic efficacy and ability to be used clinically [19][20][21]. These compounds were retrieved from the PubChem database and downloaded as a three-dimensional (3D) representation in the SDF structural format (SDF) [22].…”

Tomatidine and Patchouli Alcohol as Inhibitors of SARS-CoV-2 Enzymes (3CLpro, PLpro and NSP15) by Molecular Docking and Molecular Dynamics Simulations

“…Dimensions of the grid around the binding site vary with each of the proteins. For 6LU7, the grid box was created with size 50 × 50 × 50 xyz points, grid spacing of 0.375 Å and grid center of x, y and z dimensions of −10.729, 12 −0.058, −2.230 and 0.718 in x, y and z coordinates, respectively. Protein and ligands were set to the rigid mode during the docking procedure and a configuration file consisting for protein and ligand information along with grid box properties was prepared for executing docking using AutoDock Vina.…”

“…NF-κB-inducing kinase (NIK), Cyclooxygenase-2 (COX-2), phospholipase A2 (PLA2) and interleukin-1 receptor associated kinase 4 (IRAK-4) are important druggable targets involved in SARS-CoV-2 induced inflammatory response and can be used to screen anti-inflammatory molecules. In fact, NIK activates NF-κB2 by promoting proteolytic processing and the generation of NF-κB transcription of the targeted gene, also known to regulates both inflammation-induced and tumor-associated angiogenesis [ 12 ]. COX-2 catalyze the biosynthesis of prostaglandins, prostacylins and thromboxanes, from arachidonic acid mostly involved in pathological conditions such as inflammation, pain and fever [ 11 ].…”

Medicinal plants as immune booster in the palliative management of viral diseases: A perspective on coronavirus

“…Pneumonia Lobelia inflata (Chevallier, 2016) Eupatorium perfoliatum (Abascal & Yarnell, 2006) Asclepias tuberosa (Chevallier, 2016) Achyranthes aspera (Mukherjee et al, 2013) Lonicerae Japonica (Lin et al, 2019) Fever Tanacetum parthenium (Pareek et al, 2011) Eupatorium perfoliatum (Abascal & Yarnell, 2006) Gunnera perpensa (Lediga, 2018) Sutherlandia frutescens (Aboyade et al, 2014) Pelargonium sidoides (Patiroglu et al, 2012) Clivia miniate (Musara et al, 2021) Crinum asiaticum (Mahomoodally et al, 2021) Leucojum aestivum (Nair et al, 2017) Scadoxus puniceus (Nair et al, 2017) Pain and inflammation Houttuynia cordata (Lau et al, 2008) Sambucus nigra (Krawitz et al, 2011) Glycyrrhiza glabra (Boone et al, 2020) Alstonia scholaris (Oguntibeju, 2018) Ipomoea palmata (Karawya et al, 2010) Dry cough and dyspnea Withania somnifera (Nosalova et al, 2013) Sambucus nigra (Krawitz et al, 2011) Echinacea purpurea (Sperber et al, 2004) Allium sativum (Nantz et al, 2012) Abrus precatorius (Nantz et al, 2012) Digestive symptoms Glycyrrhiza glabra (Murray, 2020) Achillea millefolium (Boone et al, 2020) Curcuma longa (Dulbecco & Savarino, 2013) Zingiber officinalis (Dulbecco & Savarino, 2013) Cardiac involvement Terminalia arjuna (Kumar & Prabhakar, 1987) Cystus scoparius (Yarnell & Abascal, 2003) Capsicum annuum (Sanati et al, 2018) Avena sativa L (Sedighi et al, 2019) Hordeum vulgare (El-Arab et al, 2009) antioxidant (Prakash, 2020), anti-inflammatory (Herowati & Wido...…”