International Journal of Current Research and Review
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IJCRR - 10(3), February, 2018

Pages: 19-27

Date of Publication: 01-Feb-2018


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Virtual Screening and Docking Analysis of Novel Flavonoidanalogues as Antipsoriaticagents

Author: Parakh Sharma, Rohit Mishra, Babu Vakil

Category: Healthcare

Abstract:Introduction: Psoriasis is an immune-mediated chronic, inflammatory skin disease characterized by hyper proliferative keratinocytes and their infiltration into the dermis of T cells, dendritic cells, macrophages and neutrophils. There is ample evidence suggesting the key role of dysregulation of immune cells in the skin, particularly T cells, in the pathogenesis of psoriasis. Calcineurin, a calcium and calmodulin dependent serine/threonine protein phosphatase plays a major role in increasing the production of T cells and thus in the development of psoriasis. Flavonoids such as quercetin and kaempferol are known to inhibit development of psoriasis.
Objective: We have performed docking of novel designed flavonoid analogues of quercetin and kaempferol to Calcineurin by insilicoanalysis to predict their potential as antipsoriatic candidates.
Materials: Eighty analogues each of quercetin and kaempferol were designed using Schrödinger- Maestro 11 and docked with Calcineurin using PyRx software.
Results: The best binding affinities (kcal/mol) were predicted for5 quercetin analogues- Q79 (-6.1), Q78, Q77 andQ76 (-5.9) and Q44 (-4.8) and5 kaempferol analogues-K18, K40 andK44 (-7.6), K3, K48 (-7.5).
Conclusion: This study using PyRx software strongly supports the importance of computational approach in drug discovery.
The short listed novel analogues of quercetin and kaempferol follow Lipinski rule of 5, satisfying basic parameters for drug likeliness. QSAR and pharmacokinetic analysis can be deployed in future, to further characterize them. Eventually, most promising analogues can be synthesized and evaluated to verify their actual antipsoriatic activity.

Keywords: Psoriasis, Calcineurin, Kaempferol, Docking, PyRx software

DOI: 10.7324/IJCRR.2017.1035

Full Text:

INTRODUCTION
Psoriasis is an immune-mediated chronic, inflammatory skin disease characterized by hyperproliferative keratinocytes and infiltration of T cells in the dermis.[1]Advances in understanding the immune-mediated pathological mechanisms of psoriasis have opened new therapeutic avenues. [2] There are many possible protein targets in psoriasis which can be inhibited and Calcineurin (CaN) is a popular target to suppress the activation of memory CD4+T cells and their proliferation that plays an important role in psoriasis.[3]A class of drugs called calcineurin inhibitors which include compounds like cyclosporin, voclosporin and tacrolimus are already in use clinically.[4] Cyclosporin A (CsA) is known to bind to Nuclear factor of activated T cells (NF-ATc).[5,6] Thus, blocked NF-ATc transport in nucleus, in turn, blocks T-cell pathway leading to antipsoriatic activity.[7] However, extensive use of CsA is restricted by its severe side effects.[8,9]

Herbal drugs are known to have lesser side effects, ease of availability and may lend themselves as potential antipsoriatic moieties.[10] Flavonoids, have been the subject of extensive research and a variety of compounds showing beneficial effects, have been identified.[11,12] Quercetin, a flavonol, has been reported to inhibit the activity of Calcineurin in Human Embryonic Kidney cells 293 (HEK293).[13] Kaempferol, another flavonol, has also been identified as a novel calcineurin inhibitorin Jurkat cell line model.[14] Therefore, there is for exploring such flavonoids and their analogues for more potent antipsoriatic activity.

Virtual screening(VS), a process of computationally analyzing large compound libraries, to discover new drugs, has become increasingly popular tool in drug discovery research wherein the number of methods and software which use the ligand/target approach is increasing at a rapid pace.[15] The energy function that evaluates the binding free energy between protein and ligand is known as a scoring function. The steps include protein structure preparation, ligands database preparation and docking calculations.[15,16] Determining protein surface atoms and site points as well as assignment of interaction data are sometimes, internally included in the docking software like in PyRx, Schrödinger-Maestro 11 or Discovery Studio.[17]The best ligand hits are predicted by computational approaches that ‘dock’ library of ligands into the structures of target proteins and ‘score’ their potential complementarities to binding sites.[18]

The objective of the present work was to predict promising new flavonoid analogues of kaempferol and quercetin as antipsoriatic agents that will specifically bind to the target protein
calcineurin.[19]The study was performed using Maestro-11 for docking analysis.[15,17,20] The most promising predicted analogues then can be synthesized and evaluated using in vitro/in vivo testing methods. Currently there are very few effective drugs available for treatment of debilitating and life devastating disease psoriasis and work reported here is an attempt to fulfill the urgent need to identify more potent analogues of phytochemicals.[20]
 

MATERIALS AND METHODS

Selection of Calcineurin protein and optimization Protein calcineurin Protein Data Bank (PDB)ID: 1MF8 was imported from the PDB (http://www.rcsb.org/pdb) [21] andwas analyzed for its active site by discovery studio visualizer (http://accelrys.com).[22,23,24] The protein preparation wizard was used to correct the imported protein coordinates using Maestro-GUI (Schrödinger Suite).[25,26]The corrections involved adding hydrogen atoms, defining the bond orders, deleting unwanted water molecules and salts followed by optimizing hydrogen bond network. All the atoms in the system were atom-typed using the OPLS2005 force field.[26,27]
The protonation states of titratable amino acid residues were defined at pH 7.4 (physiological state) using PropKatoolin- Schrödinger Suite. For minimizing the protein in explicit water box, appropriate numbers of TIP3P water molecules along with number of ions were added to neutralize the system using Desmond module.

The protein coordinates were optimized in 3 minimization cycles, consisting of 100,000 steps with convergence criteria of 0.001 kcal/mol/Angstrom. First 1000 steps employed steepest descents minimizer and remaining steps used Conjugate- gradients minimizer.[28] The first cycle of minimization placed 25 kcal/mol/Angstrom^2 force constant. This force was reduced to 5 kcal/mol/angstrom^2 and the last cycle of minimization was performed without any restraining potentials for final energy minimization. If the system is unable to relax without any restrains after the last cycle then it is an indication that the system is not a good starting point.[29,30]
Designing and preparation of analogues: The basic structures of quercetin and kaempferol are shown in figure 1and2. The structures were retrieved from Pub Chem database (https://pubchem.ncbi.nlm.nih.gov/).[31]Theirnovel analogues were designed by maestro-11 and saved in MDL files (V2000)and were converted to SDF files used as input in PyRx software.(http://PyRx.sourceforge.net/).[32]

Docking analysis and grid generation: Open Babel tool was used for optimizing designed analogues with forcefields MMFF94 and GHEMICAL. Analogues energy was minimized by Conjugate Gradient and Steepest Descent optimization algorithms. The cycle consisted of 50000 steps with convergence criteria of 0.001 kcal/mol/Angstrom. Finally ‘all ligand’ option was used to convert the minimized files to PDBQT format to generate their atomic coordinates for docking. For docking analysis, the protein1MF8 grid box was set at the retained coordinates of cyclosporin A where center_x = -37.0035159475, center_y = 16.4330071521, and center_z = 24.2216177997.[33] Drug likeliness parameters were predicted by VLIFEMDS-QSARPro (www.vlifesciences. com).[34,35] The best interactions were visualized by Discovery Studio.[22]
RESULTS
The data for parent structure of quercetin (Figure 1-Q80) and its novel designed analogues with functional groups substitution is presented in table 1(A) whereas parent structure of kaempferol (Figure 2-K80)and data for its novel designed analogues are shown in table1(B).[36]
Table 2(AandB) shows docking scores (kcal/mol/Angstrom) retrieved from PyRx software along with parameters of drug likeliness (hydrogen bond donor/acceptor, xlogp and molecular weight) using VLIFEMDS-QSAR Pro. The PyRx software uses a measure of distance between the experimental and predicted structures to compare the accuracy of the predictions. Root mean square deviation are calculated relative to the best mode and using only movable heavy atoms. Two variants of RMSD are lb-lower bound and ub-upper bound, differing in how the atoms are matched in the distance calculation.[32]

Calcineurin protein PDB ID: 1MF8 active site analysis by discovery studio software is depicted in figure3(A)where amino acid residues val314, ala103,tyr341 and trp 352 are interacting with the known antipsoriatic drug cyclosporin A. Next, the newly designed analogues of quercetin and kaempferol from table 1 AandB were then docked at the same active site of calcineurin to predict best analogues binding mode.[33] Top scored quercetin analogues interactions with protein ID: 1MF8 are shown in Figure 3 (B-F) similarly Figure3 (G-K) shows interactions of best kaempferol analogues with 1MF8.

DISCUSSION

Some in vitro studies have shown that flavonoids like quercetin and kaempferol have anti-psoriatic activity against the calcineurin protein.[37] Such reports have shown that best docked analogues of quercetin and kaempferol do have favorable ligand-protein molecular interactions, similar to the interaction of cyclosporin A with calcineurin.[33] In our present docking analysis, datasets of 80 analogues each of kaempferol and quercetin flavonoids were docked at the active site of calcineurin protein using PyRx software. The docking data of ligand-protein molecular interactions for 5 best quercetin analogues namely Q79 (-6.1), Q78, Q77 and Q76 (-5.9) and Q44 (-4.8) and for best 5 kaempferol analogues namely K18,K40 andK44 (-7.6) and K3andK48 (-7.5)are depicted in figure 3(B-F) and (G-K), respectively.
Kartasasmita RE et al, (2010) have performed docking study using Arguslab software on inducible nitric oxide synthase (PDB ID: 1M9T) with quercetin derivatives. They predicted
more potent iNOS inhibitors than parent quercetin, asQuercetin- 3-O-acetate with -10 kcal/mol and 6,8-dichloroquercetin- 3-O-acetate with -7.49 kcal/mol binding score.[38]

Zaveri et al (2015) showed that the target protein- Deltalactam- biosynthetic de-N-acetylase protein (PDB ID: 2J13), when docked with potential ligands taken from NCI and Drug Bank databases, the best scored ligands were identified as NCI-293778 and Rofecoxib which share the common site residues as that of residues predicted in CASTp tool binding pocket predictor. [33]
From the drug likeliness analysis shown in table 2 (AandB) it becomes evident that the best analogues are in the acceptable range by Lipinski rule of 5[35] and may have similar pharmacological properties like parent structures of quercetin and kaempferol. It is hoped that some of them may possess better antipsoriatic activity.[3,5] Dash R (2015) has revealed that when docking was performed with COX-2 protein and the 12 natural flavonoids compounds, afavorable binding energy of > -8 kcal/mol in ArgusLab docking software was predicted [39]Sharma and Vakil(2017)using2D QSAR method by VLIFEMDS-QSARpro software, have predicted antipsoriatic activity for some novel analogues of quercetin and kaempferol.[40]

In line with the above discussion related to usefulness of docking studies, our work, using PyRx software, has predicted and confirmed that some novel analogues of quercetin which show similar binding scores as parent structure and kaempferol analogues too have better binding score compared to parent structure. These analogues do show favorable
drug likeliness properties and bind to the same active site of target protein calcineurin where drugs like cyclosporin A are known to bind.
CONCLUSION
This study performed with PyRx software strongly supports the importance of computational approach in early part of drug discovery research. It results in saving enormous amount of time, resources and money. The novel quercetin and kaempferol analogues follow Lipinski rule of 5. In future, 3D QSAR studies coupled with pharmacokinetic analysis can validate predicted potential of these antipsoriatic agents. Most promising analogues can be synthesized in vitro and tested on human keratinocyte cell lines and if results are satisfactory, it may prove to be rewarding experience in terms of finding more potent antipsoriatic agents.

ACKNOWLEDGMENT

Authors acknowledge the immense help received from the scholars whose articles are cited and included in references of this manuscript. The authors are also grateful to authors / editors / publishers of all those articles, journals and books from where the literature for this article has been reviewed and discussed.
Source of Funding: External funding –Nil. Internally .financed by the college

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A Study by Kumar S. et al. entitled "A Study on Clinical Spectrum, Laboratory Profile, Complications and Outcome of Pediatric Scrub Typhus Patients Admitted to an Intensive Care Unit from a Tertiary Care Hospital from Eastern India" is awarded Best Article for Vol 13 issue 09
A Study by Mardhiah Kamaruddin et al. entitled "The Pattern of Creatinine Clearance in Gestational and Chronic Hypertension Women from the Third Trimester to 12 Weeks Postpartum" is awarded Best Article for Vol 13 issue 08
A Study by Sarmila G. B. et al. entitled "Study to Compare the Efficacy of Orally Administered Melatonin and Clonidine for Attenuation of Hemodynamic Response During Laryngoscopy and Endotracheal Intubation in Gastrointestinal Surgeries" is awarded Best Article for Vol 13 issue 07
A Study by M. Muthu Uma Maheswari et al. entitled "A Study on C-reactive Protein and Liver Function Tests in Laboratory RT-PCR Positive Covid-19 Patients in a Tertiary Care Centre – A Retrospective Study" is awarded Best Article of Vol 13 issue 06 Special issue Modern approaches for diagnosis of COVID-19 and current status of awareness
A Study by Gainneos PD et al. entitled "A Comparative Evaluation of the Levels of Salivary IgA in HIV Affected Children and the Children of the General Population within the Age Group of 9 – 12 Years – A Cross-Sectional Study" is awarded Best Article of Vol 13 issue 05 Special issue on Recent Advances in Dentistry for better Oral Health
A Study by Alkhansa Mahmoud et al. entitled "mRNA Expression of Somatostatin Receptors (1-5) in MCF7 and MDA-MB231 Breast Cancer Cells" is awarded Best Article of Vol 13 issue 06
A Study by Chen YY and Ghazali SRB entitled "Lifetime Trauma, posttraumatic stress disorder Symptoms and Early Adolescence Risk Factors for Poor Physical Health Outcome Among Malaysian Adolescents" is awarded Best Article of Vol 13 issue 04 Special issue on Current Updates in Plant Biology to Medicine to Healthcare Awareness in Malaysia
A Study by Kumari PM et al. entitled "Study to Evaluate the Adverse Drug Reactions in a Tertiary Care Teaching Hospital in Tamilnadu - A Cross-Sectional Study" is awarded Best Article for Vol 13 issue 05
A Study by Anu et al. entitled "Effectiveness of Cytological Scoring Systems for Evaluation of Breast Lesion Cytology with its Histopathological Correlation" is awarded Best Article of Vol 13 issue 04
A Study by Sharipov R. Kh. et al. entitled "Interaction of Correction of Lipid Peroxidation Disorders with Oxibral" is awarded Best Article of Vol 13 issue 03
A Study by Tarek Elwakil et al. entitled "Led Light Photobiomodulation Effect on Wound Healing Combined with Phenytoin in Mice Model" is awarded Best Article of Vol 13 issue 02
A Study by Mohita Ray et al. entitled "Accuracy of Intra-Operative Frozen Section Consultation of Gastrointestinal Biopsy Samples in Correlation with the Final Histopathological Diagnosis" is awarded Best Article for Vol 13 issue 01
A Study by Badritdinova MN et al. entitled "Peculiarities of a Pain in Patients with Ischemic Heart Disease in the Presence of Individual Combines of the Metabolic Syndrome" is awarded Best Article for Vol 12 issue 24
A Study by Sindhu Priya E S et al. entitled "Neuroprotective activity of Pyrazolone Derivatives Against Paraquat-induced Oxidative Stress and Locomotor Impairment in Drosophila melanogaster" is awarded Best Article for Vol 12 issue 23
A Study by Habiba Suhail et al. entitled "Effect of Majoon Murmakki in Dysmenorrhoea (Usre Tams): A Standard Controlled Clinical Study" is awarded Best Article for Vol 12 issue 22
A Study by Ghaffar UB et al. entitled "Correlation between Height and Foot Length in Saudi Population in Majmaah, Saudi Arabia" is awarded Best Article for Vol 12 issue 21
A Study by Siti Sarah Binti Maidin entitled "Sleep Well: Mobile Application to Address Sleeping Problems" is awarded Best Article for Vol 12 issue 20
A Study by Avijit Singh"Comparison of Post Operative Clinical Outcomes Between “Made in India” TTK Chitra Mechanical Heart Valve Versus St Jude Mechanical Heart Valve in Valve Replacement Surgery" is awarded Best Article for Vol 12 issue 19
A Study by Sonali Banerjee and Mary Mathews N. entitled "Exploring Quality of Life and Perceived Experiences Among Couples Undergoing Fertility Treatment in Western India: A Mixed Methodology" is awarded Best Article for Vol 12 issue 18
A Study by Jabbar Desai et al. entitled "Prevalence of Obstructive Airway Disease in Patients with Ischemic Heart Disease and Hypertension" is awarded Best Article for Vol 12 issue 17
A Study by Juna Byun et al. entitled "Study on Difference in Coronavirus-19 Related Anxiety between Face-to-face and Non-face-to-face Classes among University Students in South Korea" is awarded Best Article for Vol 12 issue 16
A Study by Sudha Ramachandra & Vinay Chavan entitled "Enhanced-Hybrid-Age Layered Population Structure (E-Hybrid-ALPS): A Genetic Algorithm with Adaptive Crossover for Molecular Docking Studies of Drug Discovery Process" is awarded Best article for Vol 12 issue 15
A Study by Varsha M. Shindhe et al. entitled "A Study on Effect of Smokeless Tobacco on Pulmonary Function Tests in Class IV Workers of USM-KLE (Universiti Sains Malaysia-Karnataka Lingayat Education Society) International Medical Programme, Belagavi" is awarded Best article of Vol 12 issue 14, July 2020
A study by Amruta Choudhary et al. entitled "Family Planning Knowledge, Attitude and Practice Among Women of Reproductive Age from Rural Area of Central India" is awarded Best Article for special issue "Modern Therapeutics Applications"
A study by Raunak Das entitled "Study of Cardiovascular Dysfunctions in Interstitial Lung Diseas epatients by Correlating the Levels of Serum NT PRO BNP and Microalbuminuria (Biomarkers of Cardiovascular Dysfunction) with Echocardiographic, Bronchoscopic and HighResolution Computed Tomography Findings of These ILD Patients" is awarded Best Article of Vol 12 issue 13 
A Study by Kannamani Ramasamy et al. entitled "COVID-19 Situation at Chennai City – Forecasting for the Better Pandemic Management" is awarded best article for  Vol 12 issue 12
A Study by Muhammet Lutfi SELCUK and Fatma entitled "Distinction of Gray and White Matter for Some Histological Staining Methods in New Zealand Rabbit's Brain" is awarded best article for  Vol 12 issue 11
A Study by Anamul Haq et al. entitled "Etiology of Abnormal Uterine Bleeding in Adolescents – Emphasis Upon Polycystic Ovarian Syndrome" is awarded best article for  Vol 12 issue 10
A Study by entitled "Estimation of Reference Interval of Serum Progesterone During Three Trimesters of Normal Pregnancy in a Tertiary Care Hospital of Kolkata" is awarded best article for  Vol 12 issue 09
A Study by Ilona Gracie De Souza & Pavan Kumar G. entitled "Effect of Releasing Myofascial Chain in Patients with Patellofemoral Pain Syndrome - A Randomized Clinical Trial" is awarded best article for  Vol 12 issue 08
A Study by Virendra Atam et. al. entitled "Clinical Profile and Short - Term Mortality Predictors in Acute Stroke with Emphasis on Stress Hyperglycemia and THRIVE Score : An Observational Study" is awarded best article for  Vol 12 issue 07
A Study by K. Krupashree et. al. entitled "Protective Effects of Picrorhizakurroa Against Fumonisin B1 Induced Hepatotoxicity in Mice" is awarded best article for issue Vol 10 issue 20
A study by Mithun K.P. et al "Larvicidal Activity of Crude Solanum Nigrum Leaf and Berries Extract Against Dengue Vector-Aedesaegypti" is awarded Best Article for Vol 10 issue 14 of IJCRR
A study by Asha Menon "Women in Child Care and Early Education: Truly Nontraditional Work" is awarded Best Article for Vol 10 issue 13
A study by Deep J. M. "Prevalence of Molar-Incisor Hypomineralization in 7-13 Years Old Children of Biratnagar, Nepal: A Cross Sectional Study" is awarded Best Article for Vol 10 issue 11 of IJCRR
A review by Chitra et al to analyse relation between Obesity and Type 2 diabetes is awarded 'Best Article' for Vol 10 issue 10 by IJCRR. 
A study by Karanpreet et al "Pregnancy Induced Hypertension: A Study on Its Multisystem Involvement" is given Best Paper Award for Vol 10 issue 09

List of Awardees

A Study by Ese Anibor et al. "Evaluation of Temporomandibular Joint Disorders Among Delta State University Students in Abraka, Nigeria" from Vol 13 issue 16 received Emerging Researcher Award


A Study by Alkhansa Mahmoud et al. entitled "mRNA Expression of Somatostatin Receptors (1-5) in MCF7 and MDA-MB231 Breast Cancer Cells" from Vol 13 issue 06 received Emerging Researcher Award


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