Comparative modeling of retinol-binding protein-3 and retinal S-antigen in Eales’ disease and prediction of their binding sites using computational methods

Tiwari, Anshul; Trivedi, Ashish Chandra; Srivastava, Prachi; Pant, Aditya B.; Saxena, Sandeep

doi:10.1007/s12177-011-9060-z

Cited by 8 publications

(4 citation statements)

References 17 publications

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“…Three-dimensional (3D) protein structures are functionally very important and play a significant role in the progression of the disease; hence, these 3D structures are a better target for further drug designing and relative studies [24]. …”

Section: Reviewmentioning

confidence: 99%

Eales' disease - current concepts in diagnosis and management

Biswas

Ravi

Naryanasamy

et al. 2013

J OPHTH INFLAMM INFECT

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Eales' disease, first described by the British ophthalmologist Henry Eales in 1880, is characterized by three overlapping stages of venous inflammation (vasculitis), occlusion, and retinal neovascularization. Diagnosis is mostly clinical and requires exclusion of other systemic or ocular conditions that could present with similar retinal features. In recent years, immunological, molecular biological, and biochemical studies have indicated the role of human leukocyte antigen, retinal autoimmunity, Mycobacterium tuberculosis genome, and free radical-mediated damage in the etiopathogenesis of this disease. However, its etiology appears to be multifactorial. The management depends on the stage of the disease and consists of medical treatment with oral corticosteroids in the active inflammatory stage and laser photocoagulation in the advanced retinal ischemia and neovascularization stages.

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Section: Reviewmentioning

confidence: 99%

Eales' disease - current concepts in diagnosis and management

Biswas

Ravi

Naryanasamy

et al. 2013

J OPHTH INFLAMM INFECT

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“…3D structure of interphotoreceptor retinol-binding protein 3 had already been predicted in previous course of work [8].…”

Section: Docking Studiesmentioning

confidence: 64%

“…IRBP-3 transports retinoids between the retinal pigment epithelium and the photoreceptors, a critical role in the visual process [5][6][7][8]. Thus, after analyzing the significant role of this selected protein, 3D protein model structures of this protein were generated through comparative modeling approaches.…”

Section: Introductionmentioning

confidence: 99%

Protein–ligand interaction studies of retinol-binding protein 3 with herbal molecules using AutoDock for the management of Eales’ disease

Tiwari

Saxena

Pant

et al. 2012

j ocul biol dis inform

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Eales' disease is an idiopathic retinal vasculitis of the eye. The disease is predominantly characterized by recurrent vitreous hemorrhage. Interphotoreceptor retinolbinding protein 3 plays a significant role in the etiopathogenesis of this condition. It transports retinoids between the retinal pigment epithelium and the photoreceptors; hence, this protein is a potential target for docking studies. In silico data reveal that herbal molecules interact with regulatory domains of interphotoreceptor retinol-binding protein 3 (IRBP-3), resulting into significant docking score and also forms H-bond and several hydrophobic interactions between active residues of IRBP-3. These interactions between the active residues may lead to significant conformational change in that particular portion of the protein. This efficacy and suitability of ligand was determined on the basis of binding energy calculations. Ginkgolide showed minimum binding energy calculations among selected 10 other natural ligands. This fact of virtual screening for potential ligand can give new insights toward the therapeutic intonations and alterations toward the advances in treatment for Eales' disease.

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“…Furthermore, the binding affinities of predicted multi-target phytochemicals with CD163-SRCR5, Nsp4, and Nsp10 were validated by MM-PBSA binding energy calculations. This is a popular method for predicting binding free energy since it is more accurate than most scoring functions used in MD and is commonly employed in biomolecular research, including protein-ligand interactions ( 61 – 65 ). The results of MM-PBSA calculations showed that the predicted multi-target phytochemicals had strong affinity with target proteins.…”

Section: Discussionmentioning

confidence: 99%

Investigating Multi-Target Antiviral Compounds by Screening of Phytochemicals From Neem (Azadirachta indica) Against PRRSV: A Vetinformatics Approach

et al. 2022

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Porcine reproductive and respiratory syndrome virus (PRRSV) is a global health problem for pigs. PRRSV is highly destructive and responsible for significant losses to the swine industry. Vaccines are available but incapable of providing adequate and long-term protection. As a result, effective and safe strategies are urgently needed to combat the virus. The scavenger receptor cysteine-rich domain 5 (SRCR5) in porcine CD163, non-structural protein 4 (Nsp4), and Nsp10 are known to play significant roles in PRRSV infection and disease development. Therefore, we targeted these proteins to identify multi-target antiviral compounds. To identify potent inhibitors, molecular docking of neem phytochemicals was conducted; three compounds [7-deacetyl-7-oxogedunin (CID:1886), Kulactone (CID:15560423), and Nimocin (CASID:104522-76-1)] were selected based on the lowest binding energy and multi-target inhibitory nature. The efficacy and safety of the selected compounds were revealed through the pharmacokinetics analysis and toxicity assessment. Moreover, 100 ns molecular dynamics (MD) simulation was performed to evaluate the stability and dynamic behavior of target proteins and their docked complexes with selected compounds. Besides, molecular mechanics Poisson–Boltzmann surface area method was used to estimate the binding free energy of each protein-ligand complex obtained from the MD simulations and validate the affinities of selected compounds to target proteins. Based on our analysis, we concluded that the identified multi-target compounds can be utilized as lead compounds for the development of natural drugs against PRRSV. If further validated in clinical studies, these compounds can be used individually or in combination against the virus.

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Comparative modeling of retinol-binding protein-3 and retinal S-antigen in Eales’ disease and prediction of their binding sites using computational methods

Cited by 8 publications

References 17 publications

Eales' disease - current concepts in diagnosis and management

Eales' disease - current concepts in diagnosis and management

Protein–ligand interaction studies of retinol-binding protein 3 with herbal molecules using AutoDock for the management of Eales’ disease

Investigating Multi-Target Antiviral Compounds by Screening of Phytochemicals From Neem (Azadirachta indica) Against PRRSV: A Vetinformatics Approach

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