Kalirajan Rajagopal*, R. Kannan, B. Aparna, P. Varakumar, A. Pandiselvi, B. Gowramma
Department of Pharmaceutical Chemistry, JSS College of Pharmacy
(JSS Academy of Higher Education & Research), Ooty, The Nilgiris, Tamil Nadu, India.
*Corresponding Author E-mail: rkalirajan@ymail.com, rkalirajan@jssuni.edu.in
ABSTRACT:
COVID-19 is affected in more than 200 countries in the world. In this article, some pyrazole bearing 9-anilinoacridines(1a-z) were designed by in-silico studies for SARS-CoV-2 Mpro inhibitory activity. The docking for 1a-z against SARS-CoV-2 Mpro (5R82.pdb) targeting corona virus using Schrodinger suit. The Glide module is used for docking, qikprop for in-silico ADMET screening and Prime MM-GB/SA to determine binding energy of ligands. From the results, many compounds are significantly binding with SARS-CoV-2 Mpro with high G-score when compared to one of the currently recommended drug for COVID19, Hydroxychloroquine (-5.47). From results, many compounds exhibited similar interactions with SARS-CoV-2 Mpro and the aminoacids between GLN19 and GLY143 plays major role for binding. The in-silico ADMET properties are within the recommended values. The MM-GBSA calculations for most of the potent inhibitors are stable. In conclusion, 1t,m,j,o are SARS-CoV-2 Mpro inhibitors and may be useful for significant COVID19 activity after further refinement.
KEYWORDS: SARS-CoV-2 Mpro, Corona virus (COVID19), Acridine, Pyrazole, Docking studies, MM-GBSA calculation, In-silico ADMET.
INTRODUCTION:
Coronavirus Disease 2019 is mainly caused by SARS-CoV-2 which was affected in more than 200 countries1-3. According to World Health Organization, at the end of May 2021, there are more than 173 million peoples (28.8 million in India) are affected by COVID19 in the world, out of these more than 3.7 million people (3.4 lakhs in India) are died. The COVID-19 affected patients are mainly more asymptomatic4-7. So it is worthy consideration, to understand about the SARS-CoV-2, SARS CoV and MERS-CoV discuss about the inactivation of pathogen8-13.
The corona virus is vigorously spread from human to human. In the pandemic situation, to discover some drugs for COVID19 is very important14,15.
Because of COVID19 cases are increased more aggressively in day by day, the determination of some drugs for treatment of COVID19 is most important task mainly for target-based inhibitors.
In our continuous research of searching the novel compounds for various biological activities16-26 by using in-silico design and also by wet lab methods, we are designed some heterocyclic compounds and evaluation of biological activities. In Schrödinger suite LLC, there are various modules like Glide, Qikprop and Prime etc. are involved in computational methods like docking, ADMET screening and binding energy calculations etc to find the affinities and interactions which are responsible for SARS-CoV-2 Mpro inhibition. The in-silico studies may be provide key structural features to design of the potential drugs.
From the literatures, various biological activities of 9-Anilinoacridines have reported such as antimicrobial27, anticancer28-30, analgesic31, antioxidant32, antimalarial33, antileishmanial34, antinociceptive35, and antiherpes36 etc. The 9-anilinoacridine derivatives are reported as primary DNA-intercalating agent37. Likewise, the biological activities of pyrazole derivatives are also reported38-45 like anti-tumour, antimicrobial activities etc. In continuous of our previous research, we have designed 9-anilinoacridine analogs substituted with pyrazole moieties by docking studies by using the Schrodinger suit-2019-4 software. The outcomes of the research that some of the designed 9-anilinoacridines 1a-z have significant inhibitor against SARS CoV2 Mpro.
METHODS:
Molecular Docking:
The SARS-CoV-2 Mpro receptor 3D crystal structure which is co-crystallized with ligand 6-(ethylamino) pyridine-3-carbonitrile (5R82.pdb, Resolution: 1.3Å) was downloaded from RSCB protein data bank. Epic module in the Schrödinger suite 2019-4 was used to prepare protein with protein preparation wizard46. The protein is prepared by deleting unnecessary waters beyond 5 Å, addition of hydrogens and refine bond orders. Prime module was used to fill the missing chain atoms. Protein energy was minimized by Optimized Potentials for Liquid Simulations-3 (OPLS3) force field with RMSD value 0.30 Å. Then grid box are generated for the centroid of active binding site. By using ligprep module, the ligands are prepared and docked in to active site of SARS CoV-2 Mpro by Extra precision (XP) mode using Glide module. The binding affinity modes with significant G score47 have good binding affinities with receptor.
The in-silico ADMET properties for the designed compounds are calculated by qikprop module47.
MM-GBSA Binding free energy:
The binding free energy of the receptor- ligand complex was predicted and post dock energy were performed by Prime MM-GB/SA (Molecular Mechanics-Generalized Born Surface Area) of Schrödinger suit 2019-4. The OPLS3 force field was used to minimize energy for ligand-receptor complex and GB/SA with VSGB 2.0 solvent model48.
RESULTS AND DISCUSSION:
Results of in-silico methods are summarized in Table 1-3 and Figure 1-6. From the results the SARS-CoV-2 main protease inhibitory of the compounds 1a-z are greatly depends on various substituents. The pyrazole substituted 9-anilinoacridines 1a-z structures of are given in the figure 1.
The docking of the ligands with receptor active sites are performed by using Glide module of Maestro-12.2 to determine the binding affinities of the designed ligands. The ligands 1a-z were subjected for docking towards SARS-CoV-2 Mpro (5R82) to check their inhibitory property. The molecules show RMSD value 0.3. From the Table 1, the ligands 1t and 1m are significantly inhibit SARS CoV-2 Mpro with G-score greater than -5.7, when compared to Hydroxy chloroquine (G Score: -5.47) and co-crystallized ligand 6-(ethylamino)pyridine-3-carbonitrile(G Score: -4.40). . The molecules 1t and 1m have significant affinity with receptor mainly due to the lipophilic parameter and H-bonding interactions.
Figure-1 Structures of compounds 1a-z
The results were summarized in Table1. The best binding affinity modes for all the docked ligands 1a-z against SARS-CoV-2 Mpro were shown in figure 2. Almost all the compounds are bounded in the same binding pocket.
Table-1 Docking studies for Pyrazole substituted 9-anilinoacridines with SARS-CoV-2 main protease (5R82)
|
Cpd |
Glide score |
Lipophilic EvdW |
H Bond |
XP Electro |
Low MW |
Rot Penal |
XP Penalties |
|
1t |
-6.076 |
-5.424 |
-0.092 |
-1.566 |
0 |
0.136 |
|
|
1m |
-5.74 |
-5.738 |
-0.971 |
-0.09 |
-0.072 |
0.185 |
0 |
|
1j |
-5.352 |
-5.133 |
-0.724 |
-0.247 |
-0.065 |
0.184 |
0 |
|
1o |
-5.289 |
-6.195 |
-0.145 |
-0.019 |
0 |
0.207 |
0 |
|
1v |
-5.207 |
-5.845 |
-0.281 |
0.043 |
0 |
0.136 |
0 |
|
1g |
-5.17 |
-6.148 |
-0.186 |
-0.007 |
-0.025 |
0.175 |
0 |
|
1q |
-5.106 |
-5.989 |
-0.334 |
-0.032 |
0 |
0.15 |
0 |
|
1s |
-5.069 |
-5.568 |
-0.101 |
0.041 |
0 |
0.164 |
0 |
|
1w |
-5.055 |
-5.683 |
-0.042 |
-0.003 |
0 |
0.155 |
0 |
|
1d |
-4.792 |
-5.498 |
-0.38 |
-0.017 |
-0.078 |
0.187 |
0 |
|
1y |
-4.77 |
-5.823 |
-0.173 |
-0.142 |
0 |
0.162 |
0 |
|
1k |
-4.656 |
-5.675 |
-0.169 |
-0.136 |
-0.065 |
0.184 |
0 |
|
1a |
-4.535 |
-5.376 |
-0.122 |
0.042 |
0 |
0.145 |
0 |
|
1u |
-4.411 |
-4.89 |
-0.651 |
-0.413 |
0 |
0.136 |
0 |
|
1b |
-4.239 |
-5.261 |
-0.083 |
0.184 |
0 |
0.145 |
0 |
|
1f |
-4.212 |
-3.766 |
-0.7 |
-0.221 |
-0.078 |
0.187 |
0 |
|
1h |
-4.134 |
-4.789 |
-0.7 |
-0.262 |
-0.025 |
0.175 |
0 |
|
1i |
-4.134 |
-4.789 |
-0.7 |
-0.262 |
-0.025 |
0.175 |
0 |
|
1l |
-4.079 |
-5.901 |
-0.258 |
-0.056 |
0 |
0.165 |
0 |
|
1c |
-3.856 |
-4.629 |
-0.197 |
-0.387 |
0 |
0.145 |
1 |
|
1x |
-3.794 |
-4.978 |
-0.378 |
-0.346 |
0 |
0.141 |
0 |
|
1r |
-3.661 |
-4.498 |
-0.648 |
-0.265 |
-0.018 |
0.174 |
0 |
|
1e |
-3.652 |
-4.534 |
-0.7 |
-0.178 |
-0.078 |
0.187 |
0 |
|
Hydroxy chloroquine (Std) |
-5.47 |
-3.15 |
-1.75 |
-0.69 |
-0.38 |
0.5 |
0 |
|
6-(ethylamino) pyridine-3-carbonitrile (Co-crystallized ligand) |
-4.40 |
-2.9 |
-0.7 |
-0.19 |
-0.5 |
0.29 |
0 |
Fig-2 Docked poses of all compounds 1a-z with SARS-CoV-2 main protease (5R82)
From the results docking studies, many compounds have similar interactions with SARS-CoV-Mpro and the aminoacids GLN19, THR25, THR24, LEU27, THR26, HIE41, MET49, SER46, GLN189, ARG188, ASP187, VAL186, MET165, HIE164, ASN142 and GLY143 play major role in binding to the ligands. The 2D-ligand interaction of compounds 1t and 1m with SARS-CoV-2 are given in the figures 3.
1t
1m
Fig-3 Ligand Interaction of compound 1t & 1m with SARS-CoV-2 Mpro (5R82)
From the results, it was revealed that the molecules have shown agreeable Glide scores for compound 1t (-6.07 Kcal/mol) and compound 1m (-5.74 Kcal/mol) when compared to currently recommended drug for COVID19 Hydroxychloroquine (G Score -5.47). From the results, it was revealed that the compounds are showed hydrophobic and H-bond interactions with many amino acids between GLN19 and GLN189 in the binding pocket (figure 4). The compound 1m was exhibited hydrogen bonding interaction with THR118 (H-Bond lengh 2.44Ao) and ASN119 (H-Bond lengh 1.98 Ao) residues and also with some water molecules are given in the figure 5. The aromatic features of acridine and pyrazoles mainly contributed by the lipophilic interactions (figure 6).
Compound 1t (G Score: -6.08 )
Compound 1m(G Score: -5.74)
Compound 1j (G Score: -5.35)
Compound 1o(G Score: --5.29)
Figure- 4 Best affinity mode of docked compounds with SARS-CoV-2 Mpro (5R82)
Figure- 5 H-bonding interaction of compound 1m with SARS-CoV-2 Mpro (5R82)
Figure- 6 Hydrophilic/lipophilic map of compound 1t with SARS-CoV-2 Mpro (5R82)
The ADMET screening of the designed ligands are predicted in-silico by using qikprop module. From the results, the ADMET parameters for most the designed ligands are within the suggested values which are given in Table2.
The stability of docked complex was assessed by MM-GBSA binding free energy by the post scoring approach for SARS-CoV-2 Mpro (5R82) target and values are shown in the Table 3. From the MM-GBSA results, the dG bind values are in the range of -30.99 (cpd 1g) to -55.51Kcal/mol (cpd 1b) for significant active molecules and also dG lipophilic, dGvdw energy values which are positively contributing for total binding energy. The stability of docking complex is confirmed from the lowest binding energy poses which predicted by MM-GBSA free energy scoring function.
Table-2 In-silico ADMET screening for Pyrazole substituted 9-anilinoacridines
|
Compounds |
Mol. Wt. |
Dipole |
Donor HB |
Accpt HB |
QPlog o/w |
#metab |
Rule of Five |
%Human Oral Absorption |
|
1a |
491.389 |
6.387 |
2 |
2.5 |
7.016 |
2 |
1 |
100 |
|
1b |
491.389 |
5.886 |
2 |
2.5 |
7.125 |
2 |
1 |
100 |
|
1c |
491.389 |
4.139 |
2 |
2.5 |
7.129 |
2 |
1 |
100 |
|
1d |
426.52 |
6.28 |
2 |
2.5 |
6.797 |
3 |
1 |
100 |
|
1e |
426.52 |
6.672 |
2 |
2.5 |
6.873 |
3 |
1 |
100 |
|
1f |
426.52 |
6.864 |
2 |
2.5 |
6.872 |
3 |
1 |
100 |
|
1g |
442.519 |
7.985 |
2 |
3.25 |
6.716 |
3 |
1 |
100 |
|
1h |
442.519 |
7.401 |
2 |
3.25 |
6.664 |
3 |
1 |
100 |
|
1i |
442.519 |
7.401 |
2 |
3.25 |
6.664 |
3 |
1 |
100 |
|
1j |
430.483 |
4.485 |
2 |
2.5 |
6.718 |
2 |
1 |
100 |
|
1k |
430.483 |
4.006 |
2 |
2.5 |
6.789 |
2 |
1 |
100 |
|
1l |
457.49 |
8.92 |
2 |
3.5 |
5.959 |
3 |
1 |
95.518 |
|
1m |
428.492 |
7.246 |
3 |
3.25 |
5.731 |
3 |
1 |
100 |
|
1n |
440.546 |
6.821 |
2 |
2.5 |
7.232 |
3 |
1 |
100 |
|
1o |
456.546 |
5.888 |
2 |
3.25 |
7.082 |
3 |
1 |
100 |
|
1p |
456.546 |
6.604 |
2 |
3.25 |
7.133 |
3 |
1 |
100 |
|
1q |
481.383 |
6.373 |
2 |
2.5 |
7.412 |
2 |
1 |
100 |
|
1r |
444.492 |
7.838 |
4 |
4 |
5.164 |
4 |
1 |
84.659 |
|
1s |
458.518 |
7.818 |
3 |
4 |
5.985 |
4 |
1 |
100 |
|
1t |
507.388 |
7.735 |
3 |
3.25 |
6.219 |
3 |
2 |
89.691 |
|
1u |
507.388 |
6.302 |
3 |
3.25 |
6.555 |
3 |
2 |
89.131 |
|
1v |
507.388 |
7.562 |
3 |
3.25 |
6.394 |
3 |
2 |
92.096 |
|
1w |
472.545 |
5.443 |
2 |
4 |
6.819 |
4 |
1 |
100 |
|
1x |
497.382 |
6.664 |
3 |
3.25 |
6.719 |
3 |
1 |
100 |
|
1y |
460.965 |
4.058 |
2 |
2.5 |
7.297 |
3 |
1 |
100 |
|
1z |
502.571 |
7.216 |
2 |
4.75 |
6.809 |
5 |
2 |
100 |
|
Hydroxychloroquine(std) |
335.876 |
6.854 |
2 |
5.7 |
3.369 |
5 |
0 |
93.213 |
|
Recommended values |
130-725 |
1-12.5 |
0– 6 |
2-20 |
-2-6.5 |
1 – 8 |
max 4 |
>80% is high <25% is poor |
MW- Molecular weight of the molecule,
Dipole – Computed dipole moment
donorHB - Estimated number of hydrogen bonds that would be donated by the solute to water molecules in an aqueous solution.
accptHB- Estimated number of hydrogen bonds that would be accepted by the solute from water molecules in an aqueous solution
QPlogPo/w - Predicted octanol/water partition coefficient.
#metab- Number of likely metabolic reactions.
RuleOfFiveNumber of violations of Lipinski’s rule of five.
%Human- Oral absorption- Predicted human oral absorption on 0 to 100% scale.
|
Compd |
MMGBSA_ dG_Bind |
MMGBSA _dG_Bind_ Coulomb |
MMGBSA _dG_Bind_ Covalent |
MMGBSA_dG_Bind Hbond |
MMGBSA _dG_Bind_ Lipo |
MMGBSA_dG_Bind_vdW |
|
1t |
-40.8934 |
3.3008 |
-2.4885 |
0.0132 |
-17.0854 |
-47.1839 |
|
1m |
-34.5511 |
2.0548 |
0.5712 |
2.3985 |
-19.4849 |
-42.2665 |
|
1j |
-44.0509 |
-10.5992 |
-4.4535 |
1.7879 |
-12.3756 |
-32.9326 |
|
1o |
-44.1076 |
-4.3237 |
8.9740 |
-0.0282 |
-17.7875 |
-50.3493 |
|
1v |
-44.2857 |
-16.9709 |
16.0430 |
0.3358 |
-21.9537 |
-44.0201 |
|
1g |
-30.9940 |
-5.3359 |
-1.9914 |
0.8414 |
-13.8936 |
-38.7015 |
|
1q |
-44.2321 |
9.1512 |
-1.8337 |
0.0394 |
-14.2743 |
-43.0246 |
|
1s |
-39.5822 |
-6.3367 |
3.5711 |
-1.2306 |
-15.8258 |
-30.7078 |
|
1w |
-43.6721 |
2.8862 |
3.0545 |
1.3965 |
-13.8844 |
-54.1488 |
|
1d |
-37.3820 |
16.1365 |
-4.0676 |
1.4202 |
-18.9833 |
-45.4262 |
|
1y |
-35.4791 |
4.1133 |
3.1869 |
2.4399 |
-16.4169 |
-45.4761 |
|
1k |
-40.6216 |
10.8215 |
-3.1261 |
1.0787 |
-17.1737 |
-39.1478 |
|
1a |
-40.3259 |
-16.463 |
3.4383 |
-0.9626 |
-13.9651 |
-34.6412 |
|
1u |
-33.9486 |
-13.2359 |
1.7711 |
0.4676 |
-16.0638 |
-28.4883 |
|
1b |
-55.5076 |
-31.7170 |
6.7474 |
-2.6265 |
-15.2540 |
-35.6830 |
|
1f |
-49.8973 |
-35.5645 |
15.5323 |
-2.0750 |
-16.6723 |
-33.6069 |
|
1h |
-38.0701 |
-20.4441 |
0.78004 |
0.4122 |
-16.1061 |
-34.7814 |
|
1i |
-38.0701 |
-20.4441 |
0.7800 |
0.4122 |
-16.1061 |
-34.7814 |
|
1l |
-35.7492 |
15.5702 |
-8.3705 |
1.6287 |
-17.1136 |
-49.8675 |
|
1c |
-36.9850 |
1.8875 |
-0.0108 |
2.8952 |
-15.5608 |
-39.4340 |
|
1x |
-39.0372 |
-6.4394 |
3.1295 |
1.9501 |
-22.4468 |
-42.1313 |
|
1r |
-35.7532 |
-8.6493 |
2.9639 |
0.1015 |
-13.6054 |
-26.4266 |
|
1e |
-39.9204 |
-6.2329 |
-5.3781 |
1.1780 |
-15.3601 |
-40.0271 |
|
Hydroxy Chloroquine(std) |
-26.9975 |
-4.9621 |
2.1824 |
0.0011 |
-9.2894 |
-33.0622 |
CONCLUSION:
The docking study of pyrazole substituted 9-anilinoacridines 1a-z revealed that the better arrangement in the dynamic site of SARS-CoV-2 main protease target. The in-silico investigation of some lead molecules helped for the recognizing and future determinations of in-vitro and in-vivo investigations. From in-silico study, the compounds 1t and 1m may be significantly inhibit SARS-CoV-2 Mpro and may be active against COVID19 and probably helpful after further development and refinement.
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Received on 09.06.2021 Modified on 31.12.2021
Accepted on 07.05.2022 © RJPT All right reserved
Research J. Pharm. and Tech 2023; 16(2):529-534.
DOI: 10.52711/0974-360X.2023.00090