Generic placeholder image

Recent Advances in Anti-Infective Drug Discovery

Editor-in-Chief

ISSN (Print): 2772-4344
ISSN (Online): 2772-4352

Research Article

Extensive Multiple 2D-/3D-QSAR Modeling, Molecular Docking and Pharmacophoric Approaches for Piperazinylquinoline Derivatives as Respiratory Syncytial Virus Fusion Inhibitors

Author(s): Vipul P. Purohit, Bapu R. Thorat*, Suraj N. Mali, Rahul R. Wagh and Ramesh S. Yamgar

Volume 18, Issue 2, 2023

Published on: 21 December, 2022

Page: [148 - 167] Pages: 20

DOI: 10.2174/2772434418666221125090113

Price: $65

Abstract

Background: The human respiratory syncytial virus (RSV) is responsible for causing upper and lower respiratory tract infections in young children. RSV Fusion (F) protein is a surface glycoprotein that facilitates virus entry into host cells. Thus, newer designing of RSV Fusion (F) protein inhibitors is required on an urgent basis.

Methods: In the present study, we have developed statistically robust. Quantitative structure-activity relationship (QSAR) models for the effective designing of newer analogues of piperazinylquinoline derivatives (H1-H12).

Results: Our developed models were retained with high statistical parameters (R2 > 0.6 and Q2 > 0.5). Our developed pharmacophore, model (AADHRR_2) (indicating that two hydrogen bond acceptors, one hydrogen bond donor, one hydrophobic group, and two aromatic rings) is crucial for retaining the activities of piperazinylquinoline derivatives against RSV. Moreover, docking analysis of 12 new analogues on RSV pre-F in complex with 5C4 Fab (PDB ID: 5W23) and post-F trimeric protein (PDB ID: 3RRR) suggested higher affinities of these molecules against studied targets with good docking scores.

Conclusion: Thus, one can implement developed QSAR models, docking analogy and Pharmacophore models for identifications of potent leads for designed molecules as RSV Fusion (F) protein inhibitors.

Graphical Abstract

[1]
Borchers AT, Chang C, Gershwin ME, Gershwin LJ. Respiratory syncytial virus-a comprehensive review. Clin. Rev. Allergy Immunol. 2013; 45(3): 331-79.
[http://dx.doi.org/10.1007/s12016-013-8368-9] [PMID: 23575961]
[2]
Greenough A. Respiratory syncytial virus infection: clinical features, management, and prophylaxis. Curr. Opin. Pulm. Med. 2002; 8(3): 214-7.
[http://dx.doi.org/10.1097/00063198-200205000-00011] [PMID: 11981311]
[3]
Piedimonte G, Perez MK. Alternative mechanisms for respiratory syncytial virus (RSV) infection and persistence: could RSV be transmitted through the placenta and persist into developing fetal lungs? Curr. Opin. Pharmacol. 2014; 16: 82-8.
[http://dx.doi.org/10.1016/j.coph.2014.03.008] [PMID: 24810284]
[4]
Wright M, Piedimonte G. Respiratory syncytial virus prevention and therapy: Past, present, and future. Pediatr. Pulmonol. 2011; 46(4): 324-47.
[http://dx.doi.org/10.1002/ppul.21377] [PMID: 21438168]
[5]
Sigurs N. Epidemiologic and clinical evidence of a respiratory syncytial virus-reactive airway disease link. Am J Respir Crit Care Med 2001; 163(3 Pt 2)(S1): S2-6.
[http://dx.doi.org/10.1164/ajrccm.163.supplement_1.2011109] [PMID: 11254543]
[6]
Ventre K, Randolph A. Ribavirin for respiratory syncytial virus infection of the lower respiratory tract in infants and young children. Cochrane Libr. 2010; (5): CD000181
[http://dx.doi.org/10.1002/14651858.CD000181.pub4] [PMID: 20464715]
[7]
The IMpact-RSV Study Group. Palivizumab, a humanized respiratory syncytial virus monoclonal antibody, reduces hospitalization from respiratory syncytial virus infection in high-risk infants. Pediatrics 1998; 102(3): 531-7.
[http://dx.doi.org/10.1542/peds.102.3.531]
[8]
Hallak LK, Collins PL, Knudson W, Peeples ME. Iduronic acid-containing glycosaminoglycans on target cells are required for efficient respiratory syncytial virus infection. Virology 2000; 271(2): 264-75.
[http://dx.doi.org/10.1006/viro.2000.0293] [PMID: 10860881]
[9]
Zhao X, Singh M, Malashkevich VN, Kim PS. Structural characterization of the human respiratory syncytial virus fusion protein core. Proc. Natl. Acad. Sci. 2000; 97(26): 14172-7.
[http://dx.doi.org/10.1073/pnas.260499197] [PMID: 11106388]
[10]
Zhang L, Bukreyev A, Thompson CI, et al. Infection of ciliated cells by human parainfluenza virus type 3 in an in vitro model of human airway epithelium. J. Virol. 2005; 79(2): 1113-24.
[http://dx.doi.org/10.1128/JVI.79.2.1113-1124.2005] [PMID: 15613339]
[11]
a) Vaheri A. Heparin and related polyionic substances as virus inhibitors. Acta Pathol. Microbiol. Scand. 1964; 171: 171-98.
[PMID: 14227873];
b) Witvrouw M, De Clercq E. Sulfated polysaccharides extracted from sea algae as potential antiviral drugs. Gen. Pharmacol. 1997; 29(4): 497-511.
[http://dx.doi.org/10.1016/S0306-3623(96)00563-0] [PMID: 9352294];
c) Kimura K, Mori S, Tomita K, et al. Antiviral activity of NMSO3 against respiratory syncytial virus infection in vitro and in vivo. Antiviral Res. 2000; 47(1): 41-51.
[http://dx.doi.org/10.1016/S0166-3542(00)00091-7] [PMID: 10930645]
[12]
Andries K, Moeremans M, Gevers T, et al. Substituted benzimidazoles with nanomolar activity against respiratory syncytial virus. Antiviral Res. 2003; 60(3): 209-19.
[http://dx.doi.org/10.1016/j.antiviral.2003.07.004] [PMID: 14638397]
[13]
Banfati JF, Meger C, Doublet F, et al. Selection of a respiratory syncytial virus fusion inhibitor clinical candidate. 2. discovery of a morpholinopropylaminobenzimidazole derivative (TMC353121). J. Med. Chem. 2008; 51: 875-96.
[14]
Yu KL, Sin N, Civiello RL, et al. Respiratory syncytial virus fusion inhibitors. Part 4: Optimization for oral bioavailability. Bioorg. Med. Chem. Lett. 2007; 17(4): 895-901.
[http://dx.doi.org/10.1016/j.bmcl.2006.11.063] [PMID: 17169560]
[15]
Mackman RL, Sangi M, Sperandio D, et al. Discovery of an oral Respiratory Syncytial Virus (RSV) fusion inhibitor (GS-5806) and clinical proof of concept in a human RSV challenge study. J. Med. Chem. 2015; 58(4): 1630-43.
[http://dx.doi.org/10.1021/jm5017768] [PMID: 25574686]
[16]
Douglas JL, Panis ML, Ho E, et al. Inhibition of respiratory syncytial virus fusion by the small molecule VP-14637 via specific interactions with F protein. J. Virol. 2003; 77(9): 5054-64.
[http://dx.doi.org/10.1128/JVI.77.9.5054-5064.2003] [PMID: 12692208]
[17]
Feng S, Hong D, Wang B, et al. Discovery of imidazopyridine derivatives as highly potent respiratory syncytial virus fusion inhibitors. ACS Med. Chem. Lett. 2015; 6(3): 359-62.
[http://dx.doi.org/10.1021/acsmedchemlett.5b00008] [PMID: 25941547]
[18]
Cianci C, Yu KL, Combrink K, et al. Orally active fusion inhibitor of respiratory syncytial virus. Antimicrob. Agents Chemother. 2004; 48(2): 413-22.
[http://dx.doi.org/10.1128/AAC.48.2.413-422.2004] [PMID: 14742189]
[19]
Lundin A, Bergström T, Bendrioua L, Kann N, Adamiak B, Trybala E. Two novel fusion inhibitors of human respiratory syncytial virus. Antiviral Res. 2010; 88(3): 317-24.
[http://dx.doi.org/10.1016/j.antiviral.2010.10.004] [PMID: 20965215]
[20]
Wang L, Zhu Q, Xiang K, et al. Discovery of a novel respiratory syncytial virus replication inhibitor. Antimicrob. Agents Chemother. 2021; 65(6): e02576-20.
[http://dx.doi.org/10.1128/AAC.02576-20] [PMID: 33782012]
[21]
Xu J, Wu W, Chen H, Xue Y, Bao X, Zhou J. Substituted N-(4-amino-2-chlorophenyl)-5-chloro-2-hydr-oxybe-nzamide analogues potently inhibit Respiratory Syncytial Virus (RSV) replication and RSV infection-associated inflammatory responses. Bioorg. Med. Chem. 2021; 39116157
[http://dx.doi.org/10.1016/j.bmc.2021.116157]
[22]
a) Mishra VR, Ghanavatkar CW, Mali SN, Chaudhari HK, Sekar N. Schiff base clubbed benzothiazole: synthesis, potent antimicrobial and MCF-7 anticancer activity, DNA cleavage and computational study. J. Biomol. Struct. Dyn. 2019; 2019: 1-14.
[http://dx.doi.org/10.1080/07391102.2019.1621213] [PMID: 31107179];
b) Glide, The advances of computational docking. Schrodinger. NY: LLC 2017. Available from:https://www.schrodinger.com/products/glide
[23]
Zheng X, Wang L, Wang B, et al. Discovery of piperazinylquinoline derivatives as novel respiratory syncytial virus fusion inhibitors. ACS Med. Chem. Lett. 2016; 7(6): 558-62.
[http://dx.doi.org/10.1021/acsmedchemlett.5b00234] [PMID: 27326326]
[24]
Robitaille AC, Caron E, Zucchini N, et al. DUSP1 regulates apoptosis and cell migration, but not the JIP1-protected cytokine response, during respiratory syncytial virus and sendai virus infection. Sci. Rep. 2017; 7(1): 17388.
[http://dx.doi.org/10.1038/s41598-017-17689-0] [PMID: 29234123]
[25]
a) Duan J, Dixon SL, Lowrie JF, Sherman W. Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods. J. Mol. Graph. Model. 2010; 29(2): 157-70.
[http://dx.doi.org/10.1016/j.jmgm.2010.05.008] [PMID: 20579912];
b) Sastry M, Lowrie JF, Dixon SL, Sherman W. Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments. J. Chem. Inf. Model. 2010; 50(5): 771-84.
[http://dx.doi.org/10.1021/ci100062n] [PMID: 20450209];
c) Hert J, Willett P, Wilton DJ, et al. Enhancing the effectiveness of similarity-based virtual screening using nearest-neighbor information. J. Med. Chem. 2005; 48(22): 7049-54.
[http://dx.doi.org/10.1021/jm050316n] [PMID: 16250664]
[26]
Deokar H, Deokar M, Wang W, Zhang R, Buolamwini JK. QSAR studies of new pyrido[3,4-b]indole derivatives as inhibitors of colon and pancreatic cancer cell proliferation. Med. Chem. Res. 2018; 27(11-12): 2466-81.
[http://dx.doi.org/10.1007/s00044-018-2250-5]
[27]
Schrodinger release 2022-3: Phase, Schrodinger, LLC, New York, NY, 2021. Available from: https://www.schrodinger.com/citations
[28]
Mali SN, Pandey A, Thorat BR, Lai CH. Multiple 3D and 2D-quantitative structure-activity relationship models (QSAR), theoretical study and molecular modeling to identify structural requirements of imidazopyridine analogues as anti-infective agents against tuberculosis. Struct. Chem. 2022; 33(3): 679-94.
[http://dx.doi.org/10.1007/s11224-022-01879-2]
[29]
Nagre DT, Thorat BR, Mali SN, Farooqui M, Agrawal B. Experimental and computational insights into bis-indolylmethane derivatives as potent antimicrobial agents inhibiting 2, 2-dialkylglycine decarboxylase. Curr. Enzym. Inhib. 2021; 17(3): 204-16.
[http://dx.doi.org/10.2174/1573408017666210914105731]
[30]
Mali SN, Pandey A. Unveiling naturally occurring green tea polyphenol epigallocatechin-3-gallate (EGCG) targeting mycobacterium DPRE1 for anti-TB drug discovery. Eng Proc 2021; 11: 31.
[http://dx.doi.org/10.3390/ASEC2021-11185]
[31]
Ghosh S, Mali SN, Bhowmick DN, Pratap AP. Neem oil as natural pesticide: Pseudo ternary diagram and computational study. J. Indian Chem. Soc. 2021; 98(7)100088
[http://dx.doi.org/10.1016/j.jics.2021.100088]
[32]
Desale VJ, Mali SN, Thorat BR, Yamgar RS. Synthesis, admetSAR predictions, DPPH radical scavenging activity, and potent anti-mycobacterial studies of hydrazones of substituted 4-(anilino methyl) benzohydrazides (Part 2). Curr Comput Drug Des 2021; 17(4): 493-503.
[http://dx.doi.org/10.2174/1573409916666200615141047] [PMID: 32538732]
[33]
Kshatriya R, Shelke P, Mali S, Yashwantrao G, Pratap A, Saha S. Synthesis and evaluation of anticancer activity of pyrazolone appended triarylmethanes (TRAMs). ChemistrySelect 2021; 6(24): 6230-9.
[http://dx.doi.org/10.1002/slct.202101083]
[34]
Mali SN, Pandey A. Multiple QSAR and molecular modelling for identification of potent human adenovirus inhibitors. J. Indian Chem. Soc. 2021; 98(6)100082
[http://dx.doi.org/10.1016/j.jics.2021.100082]
[35]
Mali SN, Pandey A. Molecular modeling studies on 2, 4-disubstituted imidazopyridines as anti-malarials: Atom-based 3D-QSAR, molecular docking, virtual screening, in silico ADMET and theoretical analysis. J Comput Biophy Chem 2021; 20(3): 267-82.
[http://dx.doi.org/10.1142/S2737416521500125]
[36]
Chopade AR, Somade PM, Somade PP, Mali SN. Identification of anxiolytic potential of niranthin: In vivo and computational investigations. Nat. Prod. Bioprospect. 2021; 11(2): 223-33.
[http://dx.doi.org/10.1007/s13659-020-00284-8] [PMID: 33175328]
[37]
Thorat BR, Mali SN, Rani D, Yamgar RS. Synthesis, in silico and in vitro analysis of hydrazones as potential antituberculosis agents. Curr Comput Drug Des 2021; 17(2): 294-306.
[http://dx.doi.org/10.2174/15734099MTA0sOTQ3x] [PMID: 32141422]
[38]
Chopade AR, Pol RP, Patil PA, et al. An insight into the anxiolytic effects of lignans (phyllanthin and hypophyllanthin) and tannin (corilagin) rich extracts of Phyllanthus amarus: An in silico and in vivo approaches. Comb. Chem. High Throughput Screen. 2021; 24(3): 415-22.
[http://dx.doi.org/10.2174/1386207323666200605150915] [PMID: 32503404]
[39]
Mali SN, Thorat BR, Gupta DR, Pandey A. Mini-review of the importance of hydrazides and their derivatives-synthesis and biological activity. Eng Proc 2021; 11(1): 21.
[http://dx.doi.org/10.3390/ASEC2021-11157]
[40]
Nagre DT, Mali SN, Thorat BR, et al. Synthesis, in-silico potential enzymatic target predictions, pharmacokinetics, toxicity, anti-microbial and anti-inflammatory studies of bis-(2-methylindolyl) methane derivatives. Curr. Enzym. Inhib. 2021; 17(2): 127-43.
[http://dx.doi.org/10.2174/1573408017666210203203735]
[41]
Chopade AR, Pol RP, Patil PA, et al. Pharmacological and in silico investigations of anxiolytic-like effects of Phyllanthus fraternus: A probable involvement of GABA-A receptor. Curr. Enzym. Inhib. 2021; 17(1): 42-8.
[http://dx.doi.org/10.2174/1573408016999201026200650]
[42]
Anuse DG, Mali SN, Thorat BR, Yamgar RS, Chaudhari HK. Synthesis, SAR, in silico appraisal and anti-microbial study of substituted 2-aminobenzothiazoles derivatives. Curr Comput Drug Des 2021; 16(6): 802-13.
[http://dx.doi.org/10.2174/1573409915666191210125647] [PMID: 31820704]
[43]
Jadhav BS, Yamgar RS, Kenny RS, Mali SN, Chaudhari HK, Mandewale MC. Synthesis, in silico and biological studies of thiazolyl-2h-chromen-2-one derivatives as potent antitubercular agents. Curr. Computeraided Drug Des. 2020; 16(5): 511-22.
[http://dx.doi.org/10.2174/1386207322666190722162100] [PMID: 31438831]
[44]
Desale VJ, Mali SN, Chaudhari HK, Mali MC, Thorat BR, Yamgar RS. Synthesis and anti-mycobacterium study on halo-substituted 2-aryl oxyacetohydrazones. Curr. Computeraided Drug Des. 2020; 16(5): 618-28.
[http://dx.doi.org/10.2174/1573409915666191018120611] [PMID: 31648645]
[45]
Anuse DG, Thorat BR, Sawant S, Yamgar RS, Chaudhari HK, Mali SN. Synthesis, SAR, molecular docking and anti-microbial study of substituted N-bromoamido-2-aminobenzothiazoles. Curr Comput Drug Des 2020; 16(5): 530-40.
[http://dx.doi.org/10.2174/1573409915666190902143648] [PMID: 31475902]
[46]
Thorat BR, Rani D, Yamgar RS, Mali SN. Synthesis, spectroscopic, in-vitro and computational analysis of hydrazones as potential antituberculosis agents: (Part-I). Comb. Chem. High Throughput Screen. 2020; 23(5): 392-401.
[http://dx.doi.org/10.2174/1386207323999200325125858] [PMID: 32209038]
[47]
Mali SN, Pandey A. Synthesis of new hydrazones using a biodegradable catalyst, their biological evaluations and molecular modeling studies (Part-II). J Comput Biophy Chem 2022; 21(7): 857-82.
[http://dx.doi.org/10.1142/S2737416522500387]
[48]
Mali SN, Pandey A. Recent developments in medicinal and in silico applications of imidazopyridine derivatives: Special Emphasis on Malaria, Trypanosomiasis, and Tuberculosis. Chem Africa 2022; 5: 1215-36.
[http://dx.doi.org/10.1007/s42250-022-00462-w]
[49]
Pandey A, Shyamal SS, Shrivastava R, Ekka S, Mali SN. Inhibition of Plasmodium falciparum fatty acid biosynthesis (FAS-II Pathway) by natural flavonoids: A computer-aided drug designing approach. Chem Africa 2022; 5(5): 1469.
[50]
Mali SN, Tambe S, Pratap AP, Cruz JN. Molecular modeling approaches to investigate essential oils (volatile compounds) interacting with molecular targets. Essential oils. Cham: Springer 2022; pp. 417-42.
[http://dx.doi.org/10.1007/978-3-030-99476-1_18]
[51]
Kapale SS, Mali SN, Chaudhari HK. Molecular modelling studies for 4-oxo-1,4-dihydroquinoline-3-carboxamide derivatives as anticancer agents. Medicine in Drug Discovery 2019; 2100008
[http://dx.doi.org/10.1016/j.medidd.2019.100008]
[52]
Mali SN, Pandey A. Balanced QSAR and molecular modeling to identify structural requirements of imidazopyridine analogues as anti-infective agents against trypanosomiases. J Comput Biophy Chem 2022; 21(1): 83-114.
[http://dx.doi.org/10.1142/S2737416521410015]

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy