Journal of Molecular Modeling (2022) 28:212 https://doi.org/10.1007/s00894-022-05213-9 ORIGINAL PAPER Bioactive components of different nasal spray solutions may defeat SARS‑Cov2: repurposing and in silico studies Mohammad Faheem Khan1 · Waseem Ahmad Ansari1 · Tanveer Ahamad1 · Mohsin Ali Khan1 · Zaw Ali Khan1 · Aqib Sarfraz1 · Mohd Aamish Khan1 Received: 8 May 2021 / Accepted: 1 July 2022 © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2022 Abstract The recent outbreak “Coronavirus Disease 2019 (COVID-19)” is caused by fast-spreading and highly contagious severe acute respiratory syndrome coronavirus 2 (SARS-CoV2). This virus enters into the human respiratory system by binding of the viral surface spike glycoprotein (S-protein) to an angiotensin-converting enzyme2 (ACE2) receptor that is found in the nasal passage and oral cavity of a human. Both spike protein and the ACE2 receptor have been identified as promising therapeutic targets to develop anti-SARS-CoV2 drugs. No therapeutic drugs have been developed as of today except for some vaccines. Therefore, potent therapeutic agents are urgently needed to combat the COVID-19 infections. This goal would be achieved only by applying drug repurposing and computational approaches. Thus, based on drug repurposing approach, we have investigated 16 bioactive components (1–16) from different nasal spray solutions to check their efficacies against human ACE2 and SARS-CoV2 spike proteins by performing molecular docking and molecular dynamic (MD) simulation studies. In this study, three bioactive components namely ciclesonide (8), levocabastine (13), and triamcinolone acetonide (16) have been found as promising inhibitory agents against SARS-CoV2 spike and human ACE2 receptor proteins with excellent binding affinities, comparing to reference drugs such as nafamostat, arbidol, losartan, and benazepril. Furthermore, MD simulations were performed (triplicate) for 100 ns to confirm the stability of 8, 13, and 16 with said protein targets and to compute MM-PBSA-based binding-free energy calculations. Thus, bioactive components 8, 13, and 16 open the door for researchers and scientist globally to investigate them against SARS-CoV2 through in vitro and in vivo analysis. Keywords Nasal spray solution · SARS-CoV2 · In silico · Ciclesonide · Levocabastine · Triamcinolone acetonide Introduction the human angiotensin–converting enzyme 2 (ACE2) recep- tors and other targets [2]. After enters into the human, the Since the first outbreak in Wuhan, China, the novel coro- virus then synthesizes RNA via its RNA-dependent RNA navirus disease 2019 (COVID‐19) is still an unprecedented polymerase, which leads to the formation of main protease respiratory health problem, as of today July 06, 2022, caus- and complete viral assembly. Once completion of assembly, ing the death of more than ~ 6.364 millions people globally. viral particles release into the lower respiratory tract as well COVID-19 is caused by the severe acute respiratory coro- as in the external environment. In the respiratory system, navirus 2 (SARS‐CoV2), a single-stranded RNA-enveloped they cause mild respiratory symptoms, but, in some cases, virus that enters into the human body mainly through the intense inflammatory host response may triggered, leading nose. SARS-CoV2 also enters through the mouth but to a to a life-threatening acute respiratory syndrome [3]. Thus, lesser extent [1]. The virus invades the nasal and oral pas- SARS-CoV2 resides in the nasal and oral passages and then sage through the binding of its surface spike (S) protein with propagates around in the environment. Medical practition- ers, especially front-line health workers are at higher risk of getting the infection through direct contact or aerosol * Mohammad Faheem Khan [email protected] transmission of viral particles. From all over the world, researchers and health practitioners are working incessantly 1 Department of Biotechnology, Era’s Lucknow Medical to understand and to find out the cure for this deadly respira- College, Era University, Sarfarazganj, Hardoi Road, tory disease. By the date of writing this study, no specific Lucknow 226003, UP, India 13 Vol.:(0123456789) 212 Page 2 of 16 Journal of Molecular Modeling (2022) 28:212 drug is available against COVID-19. Numerous treatments COVID-19 infection. For example, remdesivir, a potent and suggestions including the use of surface disinfectants, antiviral drug of nucleotide analog has been used success- social distancing, mask, and implementation of herbal/tra- fully for the treatment of COVID-19, paving the way of ditional medicines have been studied and published to pre- repurposing approach for other approved drugs like dexa- vent SARS-CoV2 transmission [4, 5]. Therefore, effective methasone and tocilizumab. Several studies based on clinical therapeutic agents are in urgent need. New drug discovery trials have been conducted to test the efficiency of remde- or therapeutic treatment against any disease is a difficult task sivir in COVID-19 patients [14]. However, remdesivir has because it takes a long time up to 14–15 years, and expenses been approved by FDA as a recommended drug for those more than a billion dollars along with a low success (2.01%) COVID-19 patients who are on supplemental oxygen but rate [6]. Thus, these challenges are stand up like a hard wall not on mechanical ventilation. Favipiravir, lopinavir, and for the development of a new therapeutic agent to combat ritonavir have similar mechanisms to prevent SARS-CoV2 the COVID-19 globally. Keeping the time and cost in view, via inhibition of RNA-dependent RNA polymerase enzyme the repurposing approach of existing drugs may be a use- in the treatment of mild-to-moderate–infected patients; ful strategy to fight against SARS-CoV2, by boosting up however, they are not as effective as remdesivir [15, 16]. the drug development process within a short period for the Numerous protease inhibitors, originally developed as anti- treatment of COVID-19. HIV drugs, such as saquinavir, amprenavir, indinavir, and Nasal sprays are the liquid (solutions) medicines, which nelfinavir have been repurposed effectively against SARS- are delivered locally in the nasal cavity to help relieve acute CoV2 proteases enzymes as validated by many in silico and or chronic congestion (stuffiness), rhinitis, common cold, in vitro studies [17, 18]. In a study, arbidol, a potent inhibi- sinusitis, hay fever, or other types of allergies [7]. Various tor of hepatitis C and influenza virus, has shown promising types of nasal spray solutions are available in the market inhibitory effects to prevent COVID-19 infection in health as antihistaminic formulations to reduce the inflammatory care workers. Arbidol has also shown synergistic effects to effects, or as steroid formulations to relieve the symptoms of enhance immune response when combined with interferons common cold, sinusitis, hay fever, allergic rhinitis, and other in SARS-CoV2-infected patients [19, 20]. Several studies allergies, or as salt-solution (also referred to as saline nasal suggested that antimalarial drugs including chloroquine spray) that can loosen up the mucous or as topical decon- and hydroxychloroquine interrupt the binding efficiency gestant solutions to constrict the blood vessels at the time of SARS-CoV2 spike protein to the human cell membrane of inflammation process [8, 9]. Numerous studies showed receptor angiotensin–converting enzyme 2 (ACE2), improv- that the bioactive components of different nasal spray solu- ing the clinical outcomes of COVID-19 patients. In some tions have the ability to deactivate the virus within a few clinical studies, hydroxychloroquine has been found to be seconds. During the condition of the common cold, mil- effective in combination with azithromycin or more effective lions of viruses are present in the nasal passages that are alone than chloroquine in mildly infected patients. However, transmitted from person to person. The use of nasal spray FDA has raised safety concerns about the use of both drugs inhibits the transmission cycle of the virus and reduce the because of reporting side effects like irregular heart rhythm, symptoms of common cold [10]. Hypertonic saline solution blood circulation disorders, kidney, and liver problems in (NaCl) has an antiviral effect via reduction of viral load in post-COVID-19 patients [21]. the upper respiratory tract region [11]. The drug repurposing In addition, a potent antiparasitic agent named ivermectin approach has been proved as an effective way by explor- was also studied against COVID-19, but has been stopped ing the new therapeutic targets previously approved drugs by FDA in March 2021 because of its interactions with against many diseases [12]. In a recent outbreak, everybody other medications like blood thinners that may pose a risk globally was terrified about COVID-19 infection due to the of bleeding [22]. Cytokine storm, a leading cause of sever- absence of effective therapeutic agents that may act directly ity in COVID-19 patients, produces a hyperinflammatory at SARS-CoV2 encoded proteins [13]. During this time, the state which results in elevation of interleukin 1 (IL-1) and drug repurposing approach has gained much interest, or it interleukin 6 (IL-6). Thus, inhibition of cytokine storm is can be said that it is the only option over the traditional a key step in the treatment of the severity of COVID-19 drug discovery process because of shorter time, low cost, infection. Drugs in this category including anakinra (anti- and easy availability to reach us timely. It may reveal novel IL-1 receptor blocker) and tocilizumab (humanized anti-IL-6 targets for the previously approved drug to combat SARS- monoclonal antibody) have been administered successfully CoV2 at each step of transmission, infectivity, as well as in COVID-19 patients without adverse effects [23]. Besides raised co-morbidities. the above medications, corticosteroids have also been stud- Numerous FDA-approved antiviral drugs that have pre- ied. Several approved corticosteroids dexamethasone, meth- viously been used in the treatment of malaria, MERS, and ylprednisolone, and prednisolone were found to increase SARS either have been tested or are being used to cure survival rate and reduce morbidity in moderate or severe 13 Journal of Molecular Modeling (2022) 28:212 Page 3 of 16 212 COVID-19 patients [24]. Some studies conducted on hos- fluticasone furoate (2) (PubChem ID: 9854489), fluticasone pitalized individuals showed that dexamethasone effectively propionate (3) (PubChem ID: 444036), mometasone (4) reduce the deaths by 1/3 in patients who were on respiratory (PubChem ID: 441336), mometasone furoate (5) (PubChem support. However, these drugs were less effective on patients ID: 441,336), beclomethasone dipropionate (6) (PubChem without oxygen support. Interestingly, corticosteroids have ID: 21700), budesonide (7) (PubChem ID: 5281004), been found to reduce the fluid accumulation in the lungs, ciclesonide (8) (PubChem ID: 6918155), flunisolide (9) as well as alveolar damage, and thus decreased respiratory (PubChem ID: 82153), oxymetazoline (10) (PubChem ID: failure by improving hypoxia conditions [25]. Although no 4636), xylometazoline (11) (PubChem ID: 5709), azelastine study is reported on the repurposing of corticosteroids that (12) (PubChem ID: 2267), levocabastine (13) (PubChem ID: act directly on SARS-CoV2 encoded proteins to kill them, 54385), olopatadine (14) (PubChem ID: 5281071), phe- some in vitro and in vivo studies showed the effective role nylephrine (15) (PubChem ID: 6041), and triamcinolone of ciclesonide, fluticasone propionate, etc. via suppressing acetonide (16) (PubChem ID: 6436). The geometries of all ACE2 expression, and thus preventing the SARS-CoV2 ligands were optimized with the help of Discovery Studio cell entry in the nasal mucosa [26, 27]. In a previous study, 3.0 by using a clean geometry option and the CHARMm oxymetazoline and xylometazoline displayed the reduction (MMFF94) force field was applied on the ligand molecules of rhinovirus infections as shown in a study [28]. Moreover, and then saved as “sdf” or “pdb” format. The ligand prepara- povidone iodine–containing nasal spray to reduce the naso- tion was done by detecting root, set number of torsions, and pharyngeal viral load in patients with COVID-19 is under aromaticity criteria using AutoDock Tool. clinical trials [29, 30]. In this context, because of tedious and traditional methods of drug development, the drug repur- Preparation of receptors posing approach can help to develop the drugs against this disease, which can be quickly clinically applied within a To get mode of interactions of ligands within the binding short period of time. pockets of human angiotensin–converting enzyme (ACE2) In order to explore the drug repurposing approach to and spike protein of SARS-CoV-2, we retrieved the 3D struc- prevent COVID-19 transmission, the compounds (Fig. 1) tures of both the proteins with PDB-IDs 1R4L (resolution namely fluticasone (1), fluticasone furoate (2), fluticasone of crystal structure 3.00 Å) and 6LZG (resolution of crystal propionate (3), mometasone (4), mometasone furoate (5), structure 2.50 Å) respectively from the protein data bank beclomethasone dipropionate (6), budesonide (7), cicleson- (PDB) website (https://www.rcsb.org/). The 1R4L is a crys- ide (8), flunisolide (9), oxymetazoline (10), xylometazoline tal structure of human ACE2 receptor in a complex with an (11), azelastine (12), levocabastine (13), olopatadine (14), inhibitor XX5 [31]. The covalent bonds between XX5 ligand phenylephrine (15), and triamcinolone acetonide (16) were and protein-binding sites (S1 subset unit) were cleaved. The selected as a major bioactive components that are presents S1 subset is made up of interacting His374, His378, Glu375, in FDA-approved nasal spray solutions. In the present study, Thr371, Asp368, His345, Glu402, Arg514, Tyr515, Tyr510, all these ligands (1–16) were subjected to an in silico analy- His505, Arg278, Phe274 amino acids. Among them, His345, sis using molecular docking and MD simulation methods Thr371, His505 amino acids were involved in H-bond with against the active sites of spike protein of SARS-CoV2 as the ligand XX5. Similarly, the 6LZG is a crystal structure of well as human ACE2 target receptor. As per our prediction, spike protein of SARS-CoV2 with native ligand NAG [32]. this study will provide useful data that can be utilized for The S1 subdomain of 6LZG is consisted of five stranded preclinical and clinical studies to get mechanistic insights antiparallel β sheets (β1, β2, β3, β4, and β7) associates with into mode of action of nasal spray solutions with the help of α-helices and loops regions. Furthermore, these binding sites computational tools. were retrieved to ensure structural correctness by removing Hetatm and adding a hydrogen atom to the target protein receptors with the help of Discovery Studio 3.0 Visualizer Material and methods (Biovia, DS 2010). Moreover, polar hydrogen atoms and Kollman charges were also added for protein optimization Preparation of ligands via AutoDock Tool version 1.5.6 [33]. In 6LZG protein, the grid box is generated over active sites of interacting Gly446, Structure-based repurposing of clinically approved bioactive Tyr449, Gly496, Glu498, Thr500, and Gly502 amino acids. components of different nasal spray solutions were selected for screening to find out the potent anti-SARS-CoV2 agents. Molecular docking The chemical structures, as shown in Fig. 1, of bioactive components as ligands were retrieved from the PubChem Molecular docking studies of selected ligands within the site including fluticasone (1) (PubChem ID: 5311101), target receptors (1R4L and 6LZG) were performed using 13 212 Page 4 of 16 Journal of Molecular Modeling (2022) 28:212 Fig. 1 Chemical structures of active components (1–16) of various nasal spray solutions, which are available in market AutoDock Vina [34]. To initiate the molecular docking, (x = − 32.468, y = 24.877, z = − 15.026) that was centered receptor grid box was generated by putting the binding on target residues. The empirical scoring function by using site at coordinates (x = 34.933, y = 8.863, z = 23.11) with a flexible method were used for docking. Finally, the dock- dimensions of 50 Å × 50 Å × 50 Å with a suitable spac- ing results were analyzed by using the PyMol (Molecular ing around target residues for 1R4L protein. Similarly, Graphic System Version 2.4.0) visualizer and LigPlot [35] a grid box for 6LZG was also prepared having a set of softwares. dimensions of 50 Å × 50 Å × 50 Å with the coordinates 13 Journal of Molecular Modeling (2022) 28:212 Page 5 of 16 212 Molecular dynamic simulation where ΔEMM is the difference between energy of complex and sum of energy ligand and receptor, ΔGsolvent is the dif- Molecular dynamics simulation were carried out 100 ns by ference in solvation energy of the complex and sum of ligand using Desmond MD simulation package (Maestro version with receptor as well as ΔGSA is difference in surface area 12.6.144 Schrodinger 2020–4 LCC, New York USA) was used energy of complex and the sum of ligand and receptor [37]. to explore the stability of protein–ligand complexes 8-1R4L, 16-1R4L, 8-6LZG, and 13-6LZG. Each selected complex was individually solvated by placing explicit water box size Results and discussion 10 Å with single-point charges (SPC) and selected the TIP3P water model with periodic boundary condition (PBC). The To find the potential drug candidate for the treatment of force field optimized potentials for liquid simulation extended COVID-19 disease, molecular docking and molecular (OPLSe) was applied and added ions ( Na+, Cl−) to make neu- dynamic (MD) simulation of 16 bioactive components tralized the complex systems at 300 K temperature and 1 bar (1–16) of various nasal spray solutions were performed pressure with NPT ensemble. The particle mesh Ewald method against the spike protein (6LZG) of SARS-CoV2 and human was applied to determine the electrostatic interaction between receptor (1R4L) ACE2 protein. The molecular docking atoms, with Columbic cut-off radius of 9.0 Å. Furthermore, study, predicted as docking score in Table 1, has been car- Martyna–Tuckerman–Klein and Nose–Hoover chain schemes ried out by using AutoDock Vina, PyMol visualizer, and were used for the generation of barostat at 2.0 ps and thermo- LigPlot software, respectively. The results of docking scores stat 1.0 ps. Non-bonded forces were measured with r-RESPA (negative binding energies) were calculated with the help of integrators where each step was updated to the short-range AutoDock Vina to investigate the way of molecular interac- forces and each three steps was updated. The trajectories were tions within the binding pockets of protein receptors. In con- stored for analysis at 4.8-ps intervals. The activity and inter- text to find the best ligands against said protein receptors, we action of ligands with the proteins have been studied using have selected a scale of best docking score with a value > 9.0 the Desmond MD package method simulation interaction dia- for SARS-CoV2 spike (6LZG) protein and > 10.0 for human gram. MD simulations have been tracked in time by analyzing ACE2 (1R4L) protein, respectively. the RMSD positions of the atomic ligand and protein [36]. Analysis of molecular docking study MM‑GBSA calculation In order to validate the generated grid for molecular dock- The free binding energy of three ligand–protein complexes ing, the co-crystallized ligands such as XX5 of 1R4L and were performed using Prime MM-GBSA (molecular mechan- NAG of 6LZG were cleaved out and reconstructed. After ics generalized born surface area) module of Schrödinger this, they were re-docked into the binding pockets of said 2020–4 LCC, New York, USA. Furthermore, the free binding proteins via grid generation process. In our study, docking energy of docked poses of complexes were minimized and scores of ligands (1–16) show the negative binding energy calculated using OPLSe (optimized potentials for liquid simu- because of obtained molecular interactions to the active sites lation extended) force field with embedded solvation. From of said proteins. The two-dimensional (2D) views of docked 100 ns MD simulation, 40 snapshots of 25 frame at 2.5 ns poses are displayed in Figs. 2, and 3 with the distinction of of whole trajectories were obtained, and thereafter binding both hydrophilic (e.g., hydrogen bonds) and hydrophobic energy was calculated by using command thermal_mmgbsa.py forces (e.g., van der Waals and pi-pi interactions) within for each of complexes. This command extracts the Gibbs-free the binding pockets of target proteins. Additionally, Table 1 energy of binding (∆Gbinding) using MM-GBSA method as shows the docking scores along with molecular interactions. estimated by following equations: Ligand 1 (fluticasone) is used to treat allergic rhinitis [38]. In our study, it showed the − 9.1 docking score via the ΔGbinding = ΔEMM + ΔGsolvent + ΔGSA (1) formation of two hydrogen bonds with Arg273, Thr371, and ten hydrophobic bonds with Tyr127, Asn149, Trp271, ΔEMM = Ecomplex − (Eligand + Ereceptor ) (2) Phe274, His345, Pro346, Leu370, His374, Glu406, Arg518 amino acids within binding pockets of 1R4L protein. In the case of docking with 6LZG protein, this ligand showed ΔGsolvent = G(Solv)complex − G(solv)ligand + G(solv)receptor (3) the − 7.6 docking score via formation of one hydrogen bond with Tyr196 and 13 hydrophobic bonds with Leu95, Gln98, ΔGSA = G(SA)complex − G(SA)ligand + G(SA)receptor (4) Gln102, Gly205, Asp206, Glu208, Val209, Val212, Ala396, Lys562, Glu564, Pro565, Trp566 amino acids. Furthermore, ligands 2 (fluticasone furoate) and 3 (fluticasone propionate), 13 212 Page 6 of 16 Journal of Molecular Modeling (2022) 28:212 Table 1 Docking score and various molecular interactions of active components (1–16) of different nasal spray solutions against 1R4L (human ACE2) and 6LZG (SARS-CoV2 spike protein) Ligand No Receptors Docking score Interacting amino acids Hydrogen bonds Hydrophobic bonds 1 1R4L − 9.1 Arg273, Thr371 Tyr127, Asn149, Trp271, Phe274, His345, Pro346, Leu370, His374, Glu406, Arg518 6LZG − 7.6 Tyr196 Leu95, Gln98, Gln102, Gly205, Asp206, Glu208, Val209, Val212, Ala396, Lys562, Glu564, Pro565, Trp566 2 1R4L − 9.8 Arg273, His345, Lys363, Thr371 Tyr127, Asn149, Trp271, Phe274, Pro346, Asp367, Asp368, Leu370, His374, Glu406 6LZG − 8.3 Lys187, Tyr196, Trp203, Asp206 Gln102, Tyr199, Tyr202, Gly205, Asp509, Tyr510, Ser511, Arg514 3 1R4L − 8.9 Arg273, His345, Lys363, Thr371 Tyr127, Asn149, Trp271, Phe274, Pro346, Asp367, Asp368, Leu370, His374, Glu406 6LZG − 7.3 Arg403 Asp30, Asn33, His34, Glu37, Pro389, Glu406, Lys417, Tyr505 4 1R4L − 9.2 Asp367 Asp269, Phe274, Thr276, Leu370, Thr371, Glu406, Ser409, Thr445 6LZG − 7.6 Arg273 Tyr127, Leu144, Glu145, Asn149, Asp269, Trp271, Phe274, Phe504 5 1R4L − 9.9 Lys363 Asn149, Ala153, Asp269, Phe274, Thr276, Asp367, Asp368, Leu370, Thr371, Glu406, Ser409, Thr445 6LZG − 7.9 Asp350 Phe40, Ala348, His378, Phe390, Asn394, Glu398, His401 6 1R4L − 9.0 Gln98, Asn210 Leu95, Gln102, Tyr196, Tyr202,Gly205, Glu208, Val209, Gly211, Val212, Ala396, Pro565, Trp566 6LZG − 7.7 Ser43 Phe40, Ser44, Ser47, Ala348, Trp349, Asp350, Glu375, His378, Asp382, Arg393, Asn394, His401 7 1R4L − 9.5 His345 Trp271, Arg273, Phe274, pro346, Asp367, Asp368, leu370, Thr371, His374, Glu406, Arg518 6LZG − 8.4 Ser511, Arg514 Gln102, Lys187, Tyr196, Tyr199, Tyr202, Trp203, Asp206, Asp509, Tyr510 8 1R4L − 10.3 Arg273, His345, His505, Tyr515 Asn149, Ala153, Asp269, Phe274, Pro346, Asp367, Asp368, Thr371, His374, Glu375, His378, Glu402, Glu406, Arg518 6LZG − 9.3 Ser43 Phe40, Ser44, Trp69, Ala348, Asp350, His378, Asp382, Phe390, Arg393, Asn394, His401 9 1R4L − 9.5 Gln98, Asn210, Asn394 Leu95, Ala99, Glu208, Val209, Lys562, Pro565 6LZG − 8.5 Ser511, Arg514 Gln102, Tyr199, Tyr196, Tyr202, Trp203, Asp206, 10 1R4L − 7.3 Glu406, Arg518 Phe274, Pro346, Asp367, Leu370, Thr371, Thr445 6LZG − 7.0 Asp206 Leu95, Gln98, Ala99, Gln102, Tyr196, Gly205, Tyr207, Glu208, Val209, Ala396, Asn397, Glu398, Lys562, Glu564, Pro565, Trp566 11 1R4L − 7.4 Glu406 Phe274, Thr276, Asp367, Leu370, Thr371, Ser409 6LZG − 6.8 – Leu95, Gln102, Tyr196, Gly205, Asp206, Val209, Ala396, Lys562, Glu564, Trp566 12 1R4L − 9.7 – Tyr127, Asn149, Ala153, Asp269, Trp271, Phe274, Cys344, His345, Lys363, Asp367, Thr371, 6LZG − 7.8 Tyr196, Trp566 Leu95, Gln98, Gln102, Tyr202, Gly205, Asp206, Glu208, Asn210, Ala396, Lys562 13 1R4L − 9.7 His345, Asn394, Tyr385 Phe40, Ala348, Asp350, His378, Glu402, Phe504, Tyr510, Arg514, Tyr515 6LZG − 9.0 – Phe40, Leu73, Ala99, Leu100,Gln102, Asp350, Phe390, Leu391, Arg393, Asn394 14 1R4L − 9.2 Pro346, Thr371, Tyr515 Arg273, Phe274, Thr276, His345, Asp367, Asp368, His374, Thr445, His505, Arg518 6LZG − 7.2 Tyr196, Gly205, Lys562 Leu95, Gln102, Asp206, Val209, Asn394, Gly395, Ala396, Asn397, Glu564, Pro565, Trp566 15 1R4L − 6.0 Ala348, Glu402, Arg514 Thr347, His378, Phe504, Tyr510, Tyr515 6LZG − 6.1 Glu208, Asn210 Leu95, Val209, Ala396, Lys562, Glu564, Trp566 13 Journal of Molecular Modeling (2022) 28:212 Page 7 of 16 212 Table 1 (continued) Ligand No Receptors Docking score Interacting amino acids Hydrogen bonds Hydrophobic bonds 16 1R4L − 10.0 Tyr127, Arg273, His345, Thr371 Glu145, Trp271, Phe274, Lys363, Leu370, His374 6LZG − 8.2 Gln98, Gln102, Tyr202, Arg514 Tyr196, Trp203, Gly205, Asp206, Glu208, Glu398, Lys562 Benazepril 1R4L − 7.4 Tyr127, Asn149, His345 Leu144, Asp269, Trp271, Arg273, Phe274, Thr276, Pro346, Lys363, Asp367, Thr371 Losartan − 9.1 Thr371, Asp368 Asn149, Ap269, Trp271, Phe274, Lys363, Asp367, Thr445 Nafamostat 6LZG − 8.8 Gln102, Asp350, Arg393 Phe40, Leu73, Ser77, Ala99, Leu100, Phe390, Leu391 Arbidol − 7.0 Gln102 Leu95, Gln98, Ala99,Tyr196, Tyr202, Gly205, Asp206, Glu208, Lys562 * Numbering of ligands as per chemical structures displaying in Fig. 1 Fig. 2 Two-dimensional (2D) structures of ligand 8 (A) and 16 (B) bic bonds), blue circle (for nitrogen atom), white circle (for carbon within the binding pockets of 1R4L protein. The figure depicted the atom), and red circle (for oxygen atom) green dotted lines (for hydrogen bonds), red half circle (for hydropho- the ester analogs of fluticasone, are most efficient for the docking scores through the formation of molecular inter- prevention of allergic rhinitis than the previous one [39, actions with Lys187, Tyr196, Trp203, Asp206 (hydrogen 40]. As shown in Table 1, they displayed promising − 9.8 bonds), Gln102, Tyr199, Tyr202, Gly205, Asp509, Tyr510, and − 8.3 docking scores through the formation of molecular Ser511, Arg514 (hydrophobic bonds) and Arg403 (hydro- interactions with Arg273, His345, Lys363, Thr371 (hydro- gen bond), Asp30, Asn33, His34, Glu37, Pro389, Glu406, gen bonds), Tyr127, Asn149, Trp271, Phe274, Pro346, Lys417, Tyr505 (hydrophobic bonds) amino acids, respec- Asp367, Asp368, Leu370, His374, Glu406 (hydropho- tively, within the pockets of 6LZG protein. The ligand 4 bic bonds) and Lys187, Tyr196, Trp203, Asp206 (hydro- (mometasone) and its ester analog 5 (mometasone furo- gen bonds), Gln102, Tyr199, Tyr202, Gly205, Asp509, ate, Fig. 1) are well known to treat inflammatory skin dis- Tyr510, Ser511, Arg514 (hydrophobic bonds) amino acids, orders, asthma, nasal congestion, discharge, pruritus, etc. respectively, within the pockets of 1R4L protein. Both the [41, 42]. Our docking study (Table 1) claims that 4 showed ligands 2 and 3 (Table 1) also showed the − 8.3 and − 7.3 significant docking score − 9.2 and − 7.6 against 1R4L and 13 212 Page 8 of 16 Journal of Molecular Modeling (2022) 28:212 Fig. 3 Two-dimensional (2D) structures of ligand 8 (A) and 13 (B) within the binding pockets of 6LZG protein. The figure depicted the green dotted lines (for hydrogen bonds), red half circle and lines (for hydro- phobic bonds), blue circle (for nitrogen atom), white circle (for carbon atom), green circle (for fluorine atom), and red circle (for oxygen atom) 6LZG protein receptors, which were attributed to several asthma, allergic rhinitis as well as nasal polyposis [45–48]. molecular interactions with Asp367 (hydrogen bond) and In the present study, 7 showed the − 9.5 docking score via Asp269, Phe274, Thr276, Leu370, thr371, Glu406, Ser409, the formation of two hydrogen bonds with His345 and Thr445 (hydrophobic bonds) amino acids of 1R4L protein as Trp271 and ten hydrophobic bonds with Arg273, Phe274, well as Arg273 (hydrogen bond), Tyr127, Leu144, Glu145, Pro346, Asp367, Asp368, Leu370, Thr371, His374, Asn149, Asp269, Trp271, Phe274, Phe504 (hydrophobic Glu406, and Arg518 amino acids during molecular interac- bonds) amino acids of 6LZG protein, whereas 5 displayed tions with 1R4L protein. It also displayed the − 8.4 dock- the important molecular interactions (docking score − 9.9) ing score (Table 1) through formation of two hydrogen with Lys363 (hydrogen bond) and Asn149, Ala153, Asp269, bonds with Ser511, Arg514, and nine hydrophobic bonds Phe274, Thr276, Asp367, Asp368, Leu370, Thr371, Glu406, with Gln102, Lys187, Tyr196, Tyr199, Tyr202, Trp203, Ser409, Thr445 (hydrophobic bonds) amino acids within Asp206, Asp509, Tyr510 amino acids of 6LZG protein. In the pockets of 1R4L protein as well as similar molecular continuation, 8 shows the docking scores − 10.3 and − 9.3 interactions (docking score − 7.9) with Asp350 (hydrogen attributable to the presence of numerous hydrogen bonds bond), Phe40, Ala348, His378, Phe390, Asn394, Glu398, and hydrophobic bond interactions with Arg273, His345, His401 (hydrophobic bonds) amino acids within the pockets His505, Tyr515, Asn149, Ala153, Asp269, Phe274, Pro346, of 6LZG protein. Asp367, Asp368, Thr371, His374, Glu375, His378, Glu402, Ligand 6 (beclomethasone dipropionate, Fig. 1) is a Glu406, Arg518 and Ser43, Phe40, Ser44, Trp69, Ala348, diester derivative of beclomethasone steroid having pro- Asp350, His378, Asp382, Phe390, Arg393, Asn394, His401 pionyl groups at the 17- and 21-positions [43]. It has anti- amino acids within the binding pockets of 1R4L and 6LZG inflammatory and anti-asthmatic effects for the treatment protein receptors, respectively. Contrary, ligand 9 also dis- of allergic rhinitis and nasal polyps [44]. As per our study played the good docking scores − 9.5 and − 8.5 which may (Table 1), the docking scores of this ligand were found be due to the presence of many hydrogen bonds and hydro- as − 9.0 and − 7.7 that exhibited several molecular interac- phobic bonds with Gln98, Asn210, Asn394, Ala99, Glu208, tions by the presence of two hydrogen bonds with Gln98, Val209, Lys562, Pro565 amino acids of 1R4L protein as well Asn210, and 12 hydrophobic bonds with Leu95, Gln102, as with Ser511, Arg514, Gln102, Tyr199, Tyr196, Tyr202, Tyr196, Tyr202, Gly205, Glu208, Val209, Gly211, Val212, Trp203, Asp206 amino acids of 6LZG protein. Moreover, Ala396, Pro565, Trp566 amino acids of 1R4L as well as ligand 16 displayed significant docking scores with the value three hydrogen bonds with Ser43, Phe40, Ser44, and ten of − 10.0 as − 8.2 against 1R4L and 6LZG proteins respec- hydrophobic bonds with Ser47, Ala348, Trp349, Asp350, tively as compared to other ligands. It has four hydrogen Glu375, His378, Asp382, Arg393, Asn394, His401 amino bond interactions with Tyr127, Arg273, His345, Thr371, acids of 6LZG proteins, respectively. As per Fig. 1, the and six hydrophobic bond interactions with Glu145, Trp271, ligands 7 (budesonide), 8 (ciclesonide), 9 (flunisolide), Phe274, Lys363, Leu370, His374 amino acids within the and 16 (triamcinolone acetonide) are the highly oxygen- pockets of 1R4L protein as well as four hydrogen bonds ated glucocorticoid steroids having dioxapentacyclic ring with Gln98, Gln102, Tyr202, Arg514, and seven hydropho- in their basic skeleton. They are generally used as anti- bic bonds with Tyr196, Trp203, Gly205, Asp206, Glu208, inflammatory and bronchodilator drugs for the treatment of Glu398, Lys562 amino acids of 6LZG protein receptor. 13 Journal of Molecular Modeling (2022) 28:212 Page 9 of 16 212 Furthermore, Fig. 1 contains the imidazole analogs such Arg273, Phe274, Thr276, His345, Asp367, Asp368, His374, as the ligands 10 (oxymetazoline) and 11 (xylometazoline) Thr445, His505, Arg518 amino acids of 1R4L protein, which are being used as vasoconstriction agents for the treat- whereas three hydrogen bonds with Tyr196, Gly205, Lys562 ment of cold, hay fever, or other respiratory allergies [49, and 11 hydrophobic bonds with Leu95, Gln102, Asp206, 50]. They displayed low docking scores as − 7.3 and − 7.4 Val209, Asn394, Gly395, Ala396, Asn397, Glu564, Pro565, against 1R4L as well as − 7.0 and − 6.8 against 6LZG pro- Trp566 amino acids of 6LZG protein respectively. On the teins, respectively. Ligand 10 forms two hydrogen bonds other hand, ligand 15 showed molecular interactions of three with Glu406, Arg518, and six hydrophobic bonds with hydrogen bonds with Ala348, Glu402, Arg514 and five Phe274, Pro346, Asp367, Leu370, Thr371, Thr445 amino hydrophobic bonds with Thr347, His378, Phe504, Tyr510, acids, whereas 11 forms only one hydrogen bond with Tyr515 amino acids of 1R4L protein while two hydrogen Glu406 and six hydrophobic bonds with Phe274, Thr276, bond interactions with Glu208, Asn210 amino acids and six Asp367, Leu370, Thr371, Ser409 amino acids within the hydrophobic bond interactions with Leu95, Val209, Ala396, binding pockets of 1R4L protein, respectively. On the Lys562, Glu564, Trp566 amino acids were present within other hand, ligands 10 contain one hydrogen bond and 16 the binding pockets of 6LZG proteins, respectively. After hydrophobic bond interactions with Asp206, Leu95, Gln98, analysis of docking scores of all the ligands with the said Ala99, Gln102, Tyr196, Gly205, Tyr207, Glu208, Val209, proteins, we had gotten three ligands 8, 13, and 16 with Ala396, Asn397, Glu398, Lys562, Glu564, Pro565, Trp566 excellent modes of molecular interactions (Figs. 2 and 3) amino acids, whereas only ten hydrophobic bond interac- within the binding pockets of 1R4L and 6LZG proteins. tions of ligand 11 with Leu95, Gln102, Tyr196, Gly205, To this, ligands 8 and 13 showed strong binding affinities Asp206, Val209, Ala396, Lys562, Glu564, Trp566 amino against 6LZG, a SARS-CoV2 spike protein with the value of acids within of 6LZG protein were present. The ligand 12 docking score − 9.3 and − 9.0, respectively, compared to the (azelastine), a second-generation antihistamine drug, is used value of docking scores − 8.8 and − 7.0 of reference drugs as a nasal spray solution to treat allergic rhinitis and other such as nafamostat and arbidol, respectively. In addition, seasonal allergies [51]. Our docking study shows that 12 ligands 8 and 16 have shown significant binding affinities performs docking scores − 9.7 and − 7.8 against 1R4L and against 1R4L, a human ACE2 protein with the value of 6LZG proteins, respectively attributable due to the presence docking score − 10.3 and − 10.0, respectively, compared to of eleven hydrophobic bonds with Tyr127, Asn149, Ala153, the value of docking score − 7.4 and − 9.1 of reference drugs Asp269, Trp271, Phe274, Cys344, His345, Lys363, Asp367, such as benazepril and losartan respectively. Thr371 amino acids of 1R4L protein as well as two hydrogen Additionally, the protein–protein interactions at the bonds with Tyr196, Trp566, and ten hydrophobic bonds with interface of spike protein-ACE2 (S-ACE2) complex are Leu95, Gln98, Gln102, Tyr202, Gly205, Asp206, Glu208, the key players for the entry of SARS-CoV2 into the host Asn210, Ala396, Lys562 amino acids of 6LZG protein. The body. Inhibition of these interactions may be crucial to ligand 13 (levocabastine), a synthetic piperidine derivative, develop the therapeutic agents against COVID-19 disease. act as a potent H1-receptor antagonist and is extensively Lan et al. identified 13 polar amino acid residues such as used in the treatment of histamine-mediated seasonal aller- Gln24, Asp30, Glu35, Glu37, Asp38, Tyr41, Gln42, Tyr83, gic rhinitis. In our study, the binding modes of 13 within the Gln325, Glu329, Asn330, Lys353, Arg393 in human ACE2 pockets of 1R4L protein exhibit a significant docking score protein. They form favorable molecular association at the (− 9.7) due to the presence of numerous molecular interac- interface of S1 subdomain of spike glycoprotein, enhanc- tions via hydrogen bonds with His345, Asn394, Tyr385, and ing the affinity of both the receptors [54]. A study showed hydrophobic bonds with Phe40, Ala348, Asp350, His378, the numerous protein–protein interactions at the interface of Glu402, Phe504, Tyr510, Arg514, Tyr515 amino acids of S-ACE2 complex via existing of Tyr505, Ser494, Phe497, 1R4L protein. It also performs a − 9.0 docking score through Gly496, Tyr495, Tyr453, Lys403, Arg393, Phe390, Pro389, hydrophobic interactions with Phe40, leu73, Ala99, Leu100, Gln388, Ala387, Lys353, Asp38, Glu37, His34, and Asn33 Gln102, Asp350, Phe390, Leu391, Arg393, Asn394 amino amino acid residues [55]. Moreover, several experimental acids of 6LZG protein. and in silico studies have also been reported that revealed the Furthermore, as shown in Fig. 1, ligands 14 (olopatadine) presence of important interacting residues while forms the and 15 (phenylephrine), important drugs to get relief from S-ACE2 complex. [56, 57]. Recent study, based on amide nasal congestion, hay fever, and other allergic reactions [52, hydrogen/deuterium exchange mass spectrometry (HDXMS) 53], demonstrate the docking scores − 9.2 and − 6.0 against method, has indicated the main interaction sites on the pep- 1R4L as well as − 7.2 and − 6.1 against 6ZLG proteins tide chains including 340–359, 400–420, 432–452, and respectively. As of analysis, the docking score of 14 was 491–510 residues at the interface of said complex [58]. attributable to the interactions of three hydrogen bonds with Furthermore, a crystal structure of such complex has iden- Pro346, Thr371, Tyr515, and ten hydrophobic bonds with tified 24 key ACE2 residues, containing the peptides 16–45, 13 212 Page 10 of 16 Journal of Molecular Modeling (2022) 28:212 79–83, 325–330, and 350–357 that are unique to SARS- ligand properties as depicted in Table 2, and Figs. 4, 5, and CoV2 in comparison to SARS-CoV1 [59]. In our study with 6. The values in Table 2 are the mean of three runs for each comparing to above studies, it has been seen (Figs. 2 and 3) of the complexes. Although ligand 8 showed a promising that the amino acid residues (Arg393 and Phe390, Tyr505) binding affinity with the 6LZG protein receptor, still the of 1R4L and 6LZG receptors form strong molecular associa- formed complex 8-6LZG was not as stable as other com- tion with the functionalities of ligands 8, 13, and 16 respec- plexes (8-1R4L, 13-6LZG, and 16-1R4L) during the MD tively. Similarly, when we compare our docking scores, it simulation study. Thus, the complex 8-6LZG was omitted can also be seen that 8 has the most negative value (− 10.3 for further MD simulation analysis. RMSD measures the and − 9.3) of docking scores against 1R4L and 6LZG pro- average distance in between of atoms of folded protein and teins, respectively, revealing the effective binding of 8 with its value determines that how much protein conformation the key amino acid residues. It shows interacting amino acids has changed over a time period. The RMSD of 16-1R4L (His345, Asp269, Phe274, Asp367, and Asn149) as simi- and 8-1R4L complexes showed no conformational changes lar to reference drugs such as benazepril and losartan that and found well equilibrated throughout 100 ns MD simu- were found to interact with the His345, Asp269, Phe274, lation (triplicate) with the value from 1.27–4.297 Å and Asp367 and Asn149, Asp269, Phe274, Asp367 amino acids 1.235–2.897 Å respectively, displaying in Fig. 4. In a similar of 1R4L protein receptor, respectively. Moreover, 8 also con- fashion, 13-6LZG complexes exhibited very low conforma- tains Phe40 and Phe390 interacting amino acids similar to tional changes with RMSD values from 1.594 to 3.798 over reference drugs such as nafamostat and arbidol that inter- a time, indicating the promising stability and compactness acted with the Phe40 and Phe390 amino acids of the 6LZG of complexes throughout 100 ns of simulation. Furthermore, protein receptor, respectively. However, 13 shows docking RMSF analysis was observed to determine the local confor- score − 9.0 with interacting amino acids Phe40, Leu73, mational transitions and structural fluctuality in complexes Ala99, Leu100, Phe390, and Leu391, similar to reference (Fig. 4). drugs nafamostat and arbidol against 6LZG protein. Dock- Table 2 shows the RMSF values for protein as ing score − 10.0 is exhibited by 16 against 1R4L protein 0.508–6.072, 0.484–4.861, and 0.441–5.022 Å for 8-1R4L, which is due to Tyr127, Arg273, His345, Thr371, Trp271, 13-6LZG, and 16-1R4L complexes respectively, which indi- Phe274, Lys363 interacting amino acids similarly to refer- cate highest structural fluctuation. On the other hand, RMSD ence drugs benazepril and losartan against 1R4L protein. values for ligand were found as 0.736–5.245, 0.914–16.553 Overall, up to three to four hydrogen bonds are found in 8 and 3.271–7.889 Å for 8-1R4L, 13-6LZG, and 16-1R4L and 16 ligands compared to hydrogen bonds present in both complexes respectively. Thus, lowest structure fluctuation the reference drugs against 1R4L protein. On the other hand, was seen in 16-1R4L complex. The radius of gyration (Rg) two to three hydrogen bonds are present in 8 and 16 ligands is considered to be a radial distance of a group of atoms from as compared to both the reference drugs. To this analysis, their axis of rotation. Rg allows to assess the changes of ori- we found that the ligands 8, 13, and 16 are strongly bound entation in ligand conformation with respect to the protein- with the amino acid residues by more number of hydrogen binding site. Thus, it predicts the structural compactness of bonds than the reference drugs. Thus, based on our dock- a folded protein. The Rg values were found as 4.443–4.962, ing score and molecular interactions analysis, these ligands are predicted to have promising inhibition activity against both spike protein of SARS-CoV2 and human ACE2 pro- Table 2 Compilation of values obtained after MD simulation study tein receptors. The binding energy obtained in the docking for three protein-ligand complexes (8-1R4L, 13-6LZG and 16-1R4L) method was further validated by re-docking by calculating Properties Ligand–protein complexes* the binding-free energy with the help of a protein–ligand- based MMGBSA study. 8-1R4L 16-1R4L 13-6LZG RMSD (Å) 1.235–2.897 1.27–4.297 1.594–3.798 Analysis of molecular dynamic (MD) simulation RMSF (Å) 0.508–6.072 0.441–5.022 0.484–4.861 Ligand RMSD 0.736–5.245 0.914–16.553 3.271–7.889 Molecular dynamic (MD) simulation is used to investigate rGyr (Å) 4.443–4.962 3.949–4.136 4.806–5.315 the detailed conformational fluctuation in protein–ligand MolSA (Å2) 457.382–491.149 345.811–359.681 389.027–405.004 complexes over a given time of frame. In the present study, SASA (Å2) 26.005–292.032 13.533–462.456 131.459–250.302 four MD simulations (triplicate) were carried out to deter- PSA (Å2) 112.94–155.61 150.627–166.039 89.923–113.197 mine the stability of 8-1R4L, 8-6LZG, 13-6LZG, and 16- * 1R4L complexes over 100 ns duration by assessing root The presented values are the best of the triplicate MD simulation runs; RMSD, root mean square deviation; RMSF, root mean square mean square deviation (RMSD), root mean square fluctua- fluctuation; rGy, radius of gyration; MolSA, molecular surface area; tion (RMSF), and protein–ligand contact analysis together SASA, solvent-accessible-surface area; PSA, polar surface area 13 Journal of Molecular Modeling (2022) 28:212 Page 11 of 16 212 Fig. 4 In the first column, protein, and ligand RMSD values plotted from the 100 ns simulation (light blue curve) residues in interaction against simulation time 100 ns A 8-1R4l, (B) 16-1R4l, and C 13- with the ligand shown by green vertical lines; the salmon and cyan 6LZG. In the second column, the protein RMSF plots A 8-1R4l, (B) rectangles display alpha-helix and beta-strand domains, respectively. 16-1R4l, and C 13-6LZG, displaying the protein residue fluctuations The above charts are the best pose of triplicate MD simulation runs 4.806–5.315, 3.949–4.136 for the 8-1R4L, 13-6LZG, and indicating that a compact and well-folded structure of all the 6-1R4L complexes respectively. For Rg value of 8-1R4L complexes is preserved during the whole simulation. complex, a small downward fluctuation occurred from 10 Moreover, some surface properties of ligands such as to 30 ns time of frame. The Rg profiles for remaining com- intramolecular hydrogen bond (intraHB), molecular surface plexes were quite similar and have a negligible fluctuation, area (MolSA), solvent accessible surface area (SASA), and 13 212 Page 12 of 16 Journal of Molecular Modeling (2022) 28:212 Fig. 5 Ligand properties A 8-1R4l, B 16-1R4l, and C 13-6LZG (cyan blue line), and polar surface area (brown line). The presented demonstrated by RMSD (blue line), radius of gyration (green line), charts are the best of the triplicate MD simulation runs molecular surface area (orange line), solvent accessible surface area polar surface area (PSA) were also assessed to further con- 8-1R4L complex, a downward fluctuation existed from 20 firm the stability of formed protein–ligand complexes. Eval- to 30 ns and then remained steady 30 to 100 ns. For SASA uation of intraHB identifies the number of internal hydrogen properties of 13-6LZG and 16-1R4L complexes, the curve bonds in a ligand atom. MolSA describes the sub-atomic was not smooth and found shaky during 100 ns simulation. surface within the equivalent area to a van der Waals surface Furthermore, for PSA property of all the complexes except zone. SASA calculate the surface zone during the interac- 8-1R4L, the curve was uniform during whole time of frame tion of ligand with the water molecule. PSA provides the of MD simulation. In the MolSA plots for the 13-6LZG and information of ligand at which extent solvent can access the 16-1R4L complexes, the curves were steady over the whole surface area contributed only by oxygen and nitrogen atoms. simulation trajectory. MD simulation presented in Fig. 5 No intraHBs were detected for all the formed complexes. also revealed the molecular interaction profile of ligands It is evident from the MolSA, SASA, and PSA plots for 8- 8, 13, and 16 within the binding sites of SARS-CoV2- 1R4L complex, a downward fluctuation was seen at 20 ns encoded spike protein and human ACE2 protein recep- and then remained consistence during the 100-ns simulation tors. As depicted in Fig. 6, the interaction profile of formed process. For properties of MolSA, SASA, and PSA for the complexes displayed the hydrogen bond, hydrophobic 13 Journal of Molecular Modeling (2022) 28:212 Page 13 of 16 212 Fig. 6 A histogram of ligand–protein contacts analysis A 8-1R4l, B bond and water bridge, respectively. The presented values are the best 16-1R4l, and C 13-6LZG. In each column, green, violet, pink and of the triplicate MD simulation runs blue colors represent the hydrogen bond, hydrophobic bond, ionic interactions, ionic bonds, and water bridges types of interac- Tyr202, Phe390, Leu391 in 13-6LZG complex and Pro146, tions. Among the interactions, hydrogen bond is regarded as Ala153, Phe274, Pro346, Leu370 in 16-1R4L complex were vital for the stability of the protein–ligand complex through- contributors of hydrophobic bond interactions within the out the MD simulation. It was observed that nine hydro- binding pockets of protein receptors. Several water bridges gen bond formation via Glu145, Asn149, Arg273, Asn277, were also offered through interactions of Tyr127, Glu145, His345, Lys363, His505, Tyr515, Arg518 amino acids were Pro146, Asn149, Glu150, Asn154, Gly268, Asp269, found in 8-1R4L complex, whereas five and 18 hydrogen Met270, Arg273, Phe274, Thr276, Asn277, Cys344, his345, bonds formation via Gln98, Gln102, Tyr202, Asn394, Pro346, Lys363, Thr365, Asp365, Asp367, Asp370, Thr371, Lys562; and Glu145, Pro146, Asn149, Asn154, Asp269, His374, Glu375, Glu402, Glu406, Lys 441, Thr445, Thr449, Arg273, Thr276, Asn277, Ser280, Asn290, His345, Lys363, Phe504, His505, Tyr510, phe512, Tyr515, Arg518 amino Asp367, Thr371, Ser409, Lys441, Gln442, Tyr515 amino acid in 8-1R4L complex, Leu95, Gln98, Ala99, Gln102, acids in 13-6LZG, and 16-1R4L complexes, respectively. Asn103, Tyr196, Tyr202, Gly205, Asp206, Asn394, Lys562 Amino acids residues such as Trp271, Phe274, Pro346, amino acids in 13–6LZG complex, Tyr127, Glu145, Pro146, Met360, Leu370, Phe452, Leu503, Val506, Tyr510, Phe512, Asn149, Ala153, Asn154, Gly268, Asp269, Met270, Tyr515 in 8-1R4L complex, Phe40, Trp69, Ala99, Tyr196, Arg273, Phe274, Thr276, Asn277, Ser280, Asn290, Asp292, 13 212 Page 14 of 16 Journal of Molecular Modeling (2022) 28:212 Cys344, His345, Pro346, Lys363, Asp367, Asp368, thr371, possess strong in silico (molecular docking and MD simula- Glu375, His378, Glu406, Ser409, Lys441, Gln442, Thr445, tion) inhibitory effect against spike glycoprotein of SARS- Tyr515, Arg518 amino acids in 16-1R4L complex, respec- CoV2 and ACE2 receptor, a binding site in human body. tively. In addition, ionic bond interactions were maintained Our results obtained from molecular docking and simula- by Lys562 amino acids in 13-6LZG complexes. Considering tion analysis are better than the reference drugs in terms of the results obtained from MD simulation, the nasal spray binding modes in proteins. Thus, we propose that ligands 8, components 8, 13, and 16 form stable complex with 1R4L 13, and 16 will occupy the binding sites effectively within and 6LZG proteins. These complexes have shown compa- the pockets of interacting amino acids of both the targeted rable ACE2 and spike protein–inhibiting efficacy as that of receptor proteins (6LZG and 1R4L) with enhanced stability. known inhibitors such as benazepril, losartan, nafamostat, Overall, the 8-1R4L was found to be the most stable ligand and arbidol. within the pockets of receptors and could be proposed as a virtual repurpose drug to combat SARS-–CoV2 infections. Analysis of MMGBSA study However, in the future, these outcomes need to be validated using in vitro and in vivo studies. Furthermore, the MMGBSA is widely used computational method to estimate the more accurately protein–ligand binding energy than that of obtained by molecular dock- Concluding ing analysis. Therefore, we have performed this method (triplicate) to compute the final binding free energies of Sixteen active components of nasal spray solutions were 8-1R4L, 13-6LZG, and 16-1R4L complexes by combining comprehensively screened for their inhibitory effects the contribution of coulomb energy, hydrogen bonding cor- against SARS-CoV2–encoded spike and human ACE2 pro- rection energy, lipophilic energy, generalized Born electro- teins as compare to reference drugs nafamostat, arbidol, static solvation energy, as well as van der Waals energy. The losartan, and benazepril by using repurpose and computa- contribution of each of energy to the final binding energy tional approach. The ligands 8, 13, and 16 displayed the with standard deviations of three complexes are displayed promising docking scores as –9.3, –9.0, and –8.2 kcal/mol in Table 3 and fig. SI-3, 6, 9 respectively. As per results, against SARS-CoV2 spike protein along with − 10.3, − 9.7, the final binding free energy of 8-1R4L, 13-6LZG, and 16- and − 10.0 kcal/mol against human ACE2 protein, respec- 1R4L complexes were found as the values of − 72.384 kcal/ tively, indicating best three SARS-CoV-2 inhibitors among mol, − 53.889 kcal/mol, and − 55.751 kcal/mol respectively. the 16 investigated active components. The molecular dock- The complex 8-1R4L showed the lowest free binding energy ing results and stability of complexes (8-1R4L, 13-6LZG, and considered as the most stable complex compared to 13- and 16-1R4L) were validated through MD simulation over 6LZG and 16-1R4L complexes. The higher negative val- 100 ns time frame. Various protein–ligand contacts and their ues indicate the higher stability of complex. As compared properties including RMSD, RMSF, rGyr, intraHB, MolSA, to binding free energy obtained from AutoDock Vina, the SASA, and PSA were also assessed to collectively support binding-free energy for the 8-1R4L, 13-6LZG, and 16-1R4L the structural stability of the complexes. Out of best three complexes using MM-GBSA method were found to be sev- active components, 16 exhibited strongest molecular inter- enfold, sixfold, and fivefold lower respectively, signifying actions and highest stability against human ACE2 receptor even stronger binding than previously obtained. The stand- protein during whole MD simulation trajectory. Considering ard deviations were found below the value of –5.01 kcal/ the analysis of molecular docking, MD simulation, and re- mol for all the complexes except 13–6LZG (fig. SI-3, 6, 9). docking using MMGBSA approach, our results may help to From the available facts of our computed study, it can be understand the inhibitory effects of active components that concluded that the ligands 8, 13, and 16, which are present are present in different nasal spray solutions against SARS- as bioactive components in many nasal spray solutions, may CoV2. Thus, as of the absence of a therapeutic agent, we Table 3 A list of calculated Complexes ΔGBind ΔGCoul ΔGH-–bond ΔGLipo ΔGGB ΔGvdW various free energies obtained by MMGBSA study for the 8-1R4L − 72.384 − 20.748 − 1.834 − 25.559 − 40.984 − 67.814 complexes 8-1R4L, 8-6LZG, 13-6LZG -53.889 − 62.286 − 0.539 − 26.719 − 47.875 − 43.960 13-6LZG, and 16-1R4L 16-1R4L -55.751 − 24.592 − 2.949 − 17.232 − 35.862 − 48.600 * ΔGBind, binding-free energy, *ΔGCoul, Coulomb energy; ΔGH—bond, hydrogen-bonding correction energy; *ΔGLipo, lipophilic energy; *ΔGGB, generalized born electrostatic solvation energy; ΔGvdW, van der Waals energy 13 Journal of Molecular Modeling (2022) 28:212 Page 15 of 16 212 suggest here that nasal spray solutions having ciclesonide, 6. Kumar M, Taki K, Gahlot R, Sharma A, Dhangar K (2020) A levocabastine, and triamcinolone acetonide as bioactive chronicle of SARS–CoV–2: part - I – Epidemiology, diagno- sis, prognosis, transmission, and treatment. Sci Total Environ components might be used as potential therapeutic agents 734:139278 for treating COVID-19. 7. Mohs R, Greig N (2017) Drug discovery and development: role of basic biological research. Alzheimer’s Dement 3(4):651–657 Supplementary Information The online version contains supplemen- 8. Djupesland P (2012) Nasal drug delivery devices: characteristics tary material available at https://d oi.o rg/1 0.1 007/s 00894-0 22-0 5213-9. and performance in a clinical perspective—a review. Drug Deliv Transl Res 3(1):42–62 Acknowledgements We are highly thankful to all authors and man- 9. Kawauchi H, Yanai K, Wang D, Itahashi K, Okubo K (2019) Anti- agement team of Era’s Lucknow Medical College, Era University, histamines for allergic rhinitis treatment from the viewpoint of Lucknow, India, and American University of Barbados (AUB) for nonsedative properties. Int J Mol Sci 20(1):213 their assistance during this work. We also thank Mr. Hari Shanker, 10. Head K, Chong L, Hopkins C, Philpott C, Schilder A, Burton M Mr. Aohne Rizvi, and Bilal Ahmad to provide the technical support (2016) Short–course oral steroids as an adjunct therapy for chronic during this study. rhinosinusitis. Cochrane Database Syst Rev 11. Hull D, Rennie P, Noronha A et al (2007) Effects of creating a non–specific, virus–hostile environment in the nasopharynx on Author contribution W. A. A., T. A., A. S. and M. A. K. performed symptoms and duration of common cold. Acta Otorhinolaryngol the molecular docking and molecular dynamic simulation studies. M. Ital 27(2):73–77 A. K. and Z. A. K. contributed to the design the research study. M. F. 12. Ashburn T, Thor K (2004) Drug repositioning: identifying and K. supervised the study, wrote the manuscript as well as analyzed the developing new uses for existing drugs. Nat Rev Drug Discov results. 3:673e683 13. Khan Z, Karatas Y, Ceylan A, Rahman H (2021) COVID–19 and Funding This research work has been financially supported by intra- therapeutic drugs repurposing in hand: the need for collaborative mural funding at Era’s Lucknow Medical College, Era University, Luc- efforts. Pharm Hosp Clin 56:3–11 know–226003, India. 14. Gordon C, Tchesnokov E, Woolner E, Perry J, Feng J, Porter D, Gotte M (2020) Remdesivir is a direct–acting antiviral that Data availability All the docking and other computational data related inhibits RNA-dependent RNA polymerase from severe acute res- to this research work have been generated in our institute with the piratory syndrome coronavirus 2 with high potency. J Biol Chem help of the requisite systems and has been reported accordingly in the 295:6785–97 manuscript. 15. Cai Q, Yang M, Liu D, Chen J, Shu D, Xia J, Liao X, Gu Y, Cai Q, Yang Y, Shen C, Li X, Peng L, Huang D, Zhang J, Wang F, Liu J, Chen L, Chen S, Wang Z, Zhang Z, Cao R, Zhong W, Liu Y, Liu Declarations L (2020) Experimental treatment with favipiravir for COVID–19: an open–label control study. Eng Times 6:1192–8 Conflict of interest The authors declare no competing interests. 16. Hung I, Lung K, Tso E, Liu R, Chung T, Chu M, Ng Y, Lo J, Chan J, Tam A, Shum H, Chan V, Wu A, Sin K, Leung W, Law W, Lung Ethics approval We did not perform any experiments on animals while D, Sin S, Yeung P, Yip C, Zhang R, Fung A, Yan E, Leung K, Ip designing and preparing this study, so neither ethics nor informed con- J, Chu A, Chan W, Ng A, Lee R, Fung K, Yeung A, Wu T, Chan sent was necessary. The submission is according to the guidelines fol- J, Yan W, Chan W, Chan J, Lie A, Tsang O, Cheng V, Que T, Lau lowed by the journal. C, Chan K, To K, Yuen K (2020) Triple combination of inter- feron beta–1b, lopinavir–ritonavir, and ribavirin in the treatment Consent to publish Yes. of patients admitted to hospital with COVID–19: an open–label, randomised, phase 2 trial. Lancet 395:1695–1704 17. Khan S, Zia K, Ashraf S, Uddin R, Haq Z (2021) Identification of chymotrypsin–like protease inhibitors of SARS–CoV–2 via inte- grated computational approach. J Biomol Struct Dyn 39(7):1–10 References 18. Mahdi M, Motyan J, Szojka Z, Golda M, Miczi M, Tozser J (2020) Analysis of the efficacy of HIV protease inhibitors against SARS– CoV–2’s main protease. Virol J 17:190 1. Zheng J (2020) SARS–CoV–2: an emerging coronavirus that 19. Yang C, Ke C, Yue D, Li W, Hu Z, Liu W, Hu S, Wang S, Liu causes a global threat. Int J Biol Sci 16(10):1678–1685 J (2020) Effectiveness of arbidol for COVID–19 prevention in 2. Khan M, Khan M, Khan Z, Ahamad T, Ansari W (2021) In–silico health professionals. Front Public Health 8:249 study to identify dietary molecules as potential SARS–CoV–2 20. Xu P, Huang J, Zhao F, Huang W, Qi M, Lin X, Song W, Yi L agents. Lett Drug Des Discovery 18(6):562–573 (2020) Arbidol/IFN–α2b therapy for patients with corona virus 3. Ni W, Yang X, Yang D et al (2020) Role of angiotensin–convert- disease 2019: a retrospective multicenter cohort study ing enzyme 2 (ACE2) in COVID–19. Critical Care 24(1) 21. Khuroo M (2020) Chloroquine and hydroxychloroquine in coro- 4. Ansari W, Ahamad T, Khan M, Khan Z, Khan M (2022) Explo- navirus disease 2019 (COVID–19). Facts, fiction, and the hype: a ration of luteolin as potential anti–COVID–19 agent: molecular critical appraisal. Int J Antimicrob Agents 56(3):106101 docking, molecular dynamic simulation, ADMET and DFTanaly- 22. Khan S, Dhama K, Pathak M, Tiwari R, Singh B, Sah R, Bonilla- sis. Lett Drug Des Discovery 19. https://doi.org/10.2174/15701 Aldana Rodriguez-Morales A, Leblebicioglu H (2020) Ivermectin, 80819666211222151725 a new candidate therapeutic against SARS–CoV–2/COVID–19. 5. Kumar A, Ansari W, Ahamad T, Saquib M, Khan M (2021) Ann Clin Microbiol Antimicrob 19(1):23 Safe use of sodium dodecyl sulfate (SDS) to deactivate SARS– 23. Luo P, Liu Y, Qiu L, Liu X, Liu D, Li J (2020) Tocilizumab CoV–2: an evidence–based systematic review. Coronaviruses treatment in COVID19: a single center experience. J Med Virol 2(9):e120821189929 92:814–818 13 212 Page 16 of 16 Journal of Molecular Modeling (2022) 28:212 24. Singh K, Majumdar S, Singh R, Misra A (2020) Role of corticos- 41. Prakash A, Benfield P (1998) Topical Mometasone. Drugs teroid in the management of COVID–19: a systemic review and a 55:145–163 Clinician’s perspective. Diabetes Metab Syndr 14(5):971–978 42. Bousquet J (2009) Mometasone furoate: an effective anti–inflam- 25. Horby P, Lim W, Emberson J, Mafham M, Bell J, Linsell L, Sta- matory with a well-defined safety and tolerability profile in the plin N, Brightling C, Ustianowski A, Elmahi E, Prudon B, Green treatment of asthma. Int J Clin Pract 63:806–819 C, Felton T, Chadwick D, Rege K, Fegan C, Chappell L, Faust 43. Johnson M (1998) Development of fluticasone propionate and S, Jaki T, Katie J, Montgomery A, Rowan K, Juszczak, Baillei J, comparison with other inhaled corticosteroids. J Allergy Clin Haynes R, Landray M (2020) Effect of dexamethasone in hospital- Immunol 101:S434–S439 ized patients with COVID–19 preliminary report. N Engl J Med 44. Edwards T (1995) Effectiveness and safety of beclomethasone 384:693–704 dipropionate, an intranasal corticosteroid, in the treatment of 26. Nakazono A, Nakamaru Y, Ramezanpour M, Kondo T, Watanabe patients with allergic rhinitis. Clin Ther 17:1032–1041 M, Hatakeyama S, Kimura S, Honma A, Wormald PJ, Vreugde S, 45. Choulis N (2014) Dermatological drugs, topical agents, and cos- Suzuki M, Homma A (2021) Fluticasone propionate suppresses metics. Side Eff Drugs Ann 36:203–231 poly(I:C)–induced ACE2 in primary human nasal epithelial cells. 46. Deeks E, Perry C (2008) Ciclesonide. Drugs 68:1741–1770 Front Cell Infect Microbiol 11:655666 47. Spector S (1997) Overview of comorbid associations of allergic 27. Finney L, Glanville N, Farne H, Aniscenko J, Fenwick P, Kemp rhinitis. J Allergy Clin Immunol 99:S773–S780 S, Trujillo-Torralbo M, Loo S, Calderazzo M, Wedzicha J, Mal- 48. Stokes M, Amorosi S, Thompson D, Dupclay L, Garcia J, Georges lia P, Bartlett N, Johnston S, Singanayagam A (2020) Inhaled G (2004) Evaluation of patients’ preferences for triamcinolone corticosteroids downregulate the SARS–CoV–2 receptor ACE2 acetonide aqueous, fluticasone propionate, and mometasone furo- in COPD through suppression of type I interferon. J Allergy Clin ate nasal sprays in patients with allergic rhinitis. Otolaryngol Head Immunol 147(2):510–519 Neck Surg 131:225–231 28. Ramalingam S, Graham C, Dove J, Morrice L, Sheikh A (2019) 49. Dokuyucu R, Gokce H, Sahan M, Sefil F, Tas Z, Tutuk O, Ozturk A pilot, open labelled, randomised controlled trial of hypertonic A, Tumer C, Cevik C (2015) Systemic side effects of locally used saline nasal irrigation and gargling for the common cold. Sci Rep oxymetazoline. Int J Clin Exp Med 8(2):2674–2678 9(1) 50. Graf C, Bernkop-Schnürch A, Egyed A, Koller C, Prieschl-Gras- 29. Winther B, Buchert D, Turner R, Hendley J, Tschaikin M (2010) sauer E, Morokutti-Kurz M (2018) Development of a nasal spray Decreased rhinovirus shedding after intranasal oxymetazoline containing xylometazoline hydrochloride and iota–carrageenan application in adults with induced colds compared with intranasal for the symptomatic relief of nasal congestion caused by rhinitis saline. Am J Rhinol Allergy 24(5):374–377 and sinusitis. Int J Gen Med 11:275–283 30. Guenezan J, Garcia M, Strasters D (2021) Povidone iodine mouth- 51. Horak F (2008) Effectiveness of twice daily azelastine nasal spray wash, gargle, and nasal spray to reduce nasopharyngeal viral load in patients with seasonal allergic rhinitis. Ther Clin Risk Manag in patients with COVID–19. JAMA Otolaryngol Head Neck Surg 4:1009–1022 147(4):400 52. Ratner P, Hampel F, Amar N, van Bavel J, Mohar D, Marple 31. Towler P, Staker B, Prasad S, Menon S, Tang J, Parsons T, B, Roland P, Wall G, Brubaker M, Drake M, Turner D, Silver Ryan D, Fisher M, Williams D, Dales N, Patane M, Pantoliano L (2005) Safety and efficacy of olopatadine hydrochloride nasal M (2004) ACE2 X-ray structures reveal a large hinge–bending spray for the treatment of seasonal allergic rhinitis to mountain motion important for inhibitor binding and catalysis. J Biol Chem cedar. Ann Allergy Asthma Immunol 95:474–479 279(17):17996–18007 53. Meltzer E (2010) Treatment of congestion in upper respiratory 32. Wang Q, Zhang Y, Wu L, Niu S, Song C, Zhang Z, Lu G, Qiao C, diseases. Int Gen Med 3:69–91 Hu Y, Yuen K, Wang Q, Zhou H, Yan J, Qi J (2020) Structural and 54. Lan J, Ge J, Yu J, Shan S, Zhou H, Fan S, Zhang Q, Shi X, Wang functional basis of SARS–CoV–2 entry by using human ACE2. Q, Zhang L, Wang X (2020) Structure of the SARS–CoV-2 spike Cell 181(4):894–904 receptor–binding domain bound to the ACE2 receptor. Nature 33. Morris G, Huey R, Lindstrom W, Sanner M, Belew R, Good- 581:215–220 sell D, Olson A (2009) AutoDock4 and AutoDockTools4: auto- 55. Yan R, Zhang Y, Li Y, Xia L, Guo Y, Zhou Q (2020) Structural mated docking with selective receptor flexibility. J Comput Chem basis for the recognition of SARS–CoV–2 by full–length human 30(16):2785–2791 ACE2. Science 367:1444–1448 34. Trott O, Olson A (2010) AutoDock Vina: improving the speed 56. Pirolli D, Righino B, De Rosa M (2021) Targeting SARS- CoV-2 and accuracy of docking with a new scoring function, efficient spike protein/ACE2 protein-protein interactions: a computational optimization, and multithreading. J Comput Chem 31(2):455–461 study. Mol Informa 40:2060080 35. Wallace A, Laskowski R, Thornton J (1995) LIGPLOT: a program 57. Ahmad I, Pawara R, Surana S, Patel H (2021) The repurposed to generate schematic diagrams of protein–ligand interactions. ACE2 inhibitors: SARS–CoV–2 entry blockers of Covid-19. Top Protein Eng 8(2):127–134 Curr Chem 379(40) 36. Ivanova L, Tammiku-Taul J, García-Sosa A, Sidorova Y, Saarma 58. Raghuvamsi P, Tulsian N, Samsudin F, Qian X, Purushotorman K, M, Karelson M (2018) Molecular dynamics simulations of the Yue G, Kozma M, Hwa W, Lescar J, Bond P, MacAry P, Anand interactions between glial cell line–derived neurotrophic factor G (2021) SARS-CoV-2 S protein: ACE2 interaction reveals novel family receptor GFRα1 and small–molecule ligands. ACS Omega allosteric targets. eLife 10: e63646 3(9):11407–11414 59. Wang Y, Liu M, Gao J (2020) Enhanced receptor binding of 37. Li J, Abel R, Zhu K, Cao Y, Zhao S, Friesner RA (2011) The SARS-CoV-2 through networks of hydrogen–bonding and hydro- VSGB 2.0 model: a next generation energy model for high–resolu- phobic interactions. PNAS 117:13967–13974 tion protein structure modeling. Proteins 79(10):2794–2812 38. Sur D, Scandale S (2010) Treatment of allergic rhinitis. Am Fam Publisher's note Springer Nature remains neutral with regard to Physician 81(12):1440–1446 jurisdictional claims in published maps and institutional affiliations. 39. Giavina-Bianchi P (2008) Fluticasone furoate nasal spray in the treatment of allergic rhinitis. Ther Clin Risk Manag 4:465–472 40. Scadding G (2010) Seasonal allergic rhinitis: fluticasone propion- ate and fluticasone furoate therapy evaluated. J Asthma Allergy 17 13
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