1
|
França TCC, Bastos LDC, Cuya T, Sirouspour M, Chacón-Huete F, Bendahan D, Forgione P. Microwave-assisted Synthesis and Docking Studies of Phenylureas as Candidates for the Drug Design Against the Biological Warfare Agent Yersinia Pestis. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180816666190710144212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Bubonic plague is amongst the diseases with the highest potential for being
used in biological warfare attacks today. This disease, caused by the bacterium Yersina pestis, is
highly infectious and can achieve 100% of fatal victims when in its most dangerous form. Besides,
there is no effective vaccine, and the chemotherapy available today against plague is ineffective if
not administered at the beginning of the infection.
Objective:
Willing to contribute for changing this reality we propose here new phenylureas as candidates
for the drug design against plague meant to target the enzyme dihydrofolate reductase from
Y. pestis (YpDHFR).
Methods:
Seven phenylureas, four of them new, were synthesized, following synthetic routes
adapted from procedures available in the literature, and using microwave irradiation. After, they
were submitted to docking studies inside YpDHFR and human DHFR (HssDHFR) in order to check
their potential as selective inhibitors.
Results:
Our results revealed four new phenylureas and a new synthetic route for this kind of molecule
using microwave irradiation. Also, our docking studies showed that these compounds are capable
of binding to both HssDHFR and YpDHFR, with U1 - U4 and U23 showing more selectivity for
HssDHFR and U7, U8 being more selective towards YpDHFR.
Conclusion:
We reported the synthesis with good yields of seven phenylureas, following a simple
and clean alternative synthetic route using microwave irradiation. Further molecular docking studies
of our compounds suggested that two are capable of binding more selectivity to YpDHFR, qualifying
as potential candidates for the drug design of new drugs against plague.
Collapse
Affiliation(s)
- Tanos Celmar Costa França
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | - Leonardo da Costa Bastos
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil
| | - Teobaldo Cuya
- Faculty of Technology, Department of Mathematics, Physics and Computation, University of the State of Rio de Janeiro, Resende, RJ, Brazil
| | - Mehdi Sirouspour
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC, Canada
| | - Franklin Chacón-Huete
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC, Canada
| | - David Bendahan
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC, Canada
| | - Pat Forgione
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC, Canada
| |
Collapse
|
2
|
Bagchi S, Kumar M, Sharma A. A multilayer screening approach toward the discovery of novel Pf-DHFR inhibitors. Comput Biol Chem 2016; 62:36-46. [PMID: 27061145 DOI: 10.1016/j.compbiolchem.2016.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 02/26/2016] [Accepted: 03/20/2016] [Indexed: 10/22/2022]
Abstract
A small yet diverse xanthone library was build and computationally docked against wild type Pf-DHFR by Molegro Virtual Docker (MolDock). For analysis of results an integrated approach based on re-ranking, scaling (based on heavy atom counts), pose clustering and visual inspection was implemented. Standard methods such as self-docking (for docking), EF analysis, average rank determinations (for size normalization), and cluster quality indices (for pose clustering) were used for validation of results. Three compounds X5, X113A and X164B displayed contact footprints similar to the known inhibitors with good scores. Finally, 16 compounds were extracted from ZINC data base by similarity based screening, docking score and drug/lead likeness. Out of these 16 compounds, 11 displayed very close contact footprints to experimentally known inhibitors, indicating there potential utility in further drug discovery efforts.
Collapse
Affiliation(s)
- Sourav Bagchi
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Manoj Kumar
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Anuj Sharma
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, India.
| |
Collapse
|
3
|
Analyses of the Binding between Water Soluble C60 Derivatives and Potential Drug Targets through a Molecular Docking Approach. PLoS One 2016; 11:e0147761. [PMID: 26829126 PMCID: PMC4735121 DOI: 10.1371/journal.pone.0147761] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/07/2016] [Indexed: 11/19/2022] Open
Abstract
Fullerene C60, a unique sphere-shaped molecule consisting of carbon, has been proved to have inhibitory effects on many diseases. However, the applications of C60 in medicine have been severely hindered by its complete insolubility in water and low solubility in almost all organic solvents. In this study, the water-soluble C60 derivatives and the C60 binding protein’s structures were collected from the literature. The selected proteins fall into several groups, including acetylcholinesterase, glutamate racemase, inosine monophosphate dehydrogenase, lumazine synthase, human estrogen receptor alpha, dihydrofolate reductase and N-myristoyltransferase. The C60 derivatives were docked into the binding sites in the proteins. The binding affinities of the C60 derivatives were calculated. The bindings between proteins and their known inhibitors or native ligands were also characterized in the same way. The results show that C60 derivatives form good interactions with the binding sites of different protein targets. In many cases, the binding affinities of C60 derivatives are better than those of known inhibitors and native ligands. This study demonstrates the interaction patterns of C60 derivatives and their binding partners, which will have good impact on the fullerene-based drug discovery.
Collapse
|
4
|
Bastos LDC, de Souza FR, Guimarães AP, Sirouspour M, Cuya Guizado TR, Forgione P, Ramalho TC, França TCC. Virtual screening, docking, and dynamics of potential new inhibitors of dihydrofolate reductase from Yersinia pestis. J Biomol Struct Dyn 2016; 34:2184-98. [DOI: 10.1080/07391102.2015.1110832] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Leonardo da Costa Bastos
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ 22290-270, Brazil
| | - Felipe Rodrigues de Souza
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ 22290-270, Brazil
| | - Ana Paula Guimarães
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ 22290-270, Brazil
- Department of Chemistry, Federal University of Viçosa, Viçosa, MG 36570-000 Brazil
| | - Mehdi Sirouspour
- Department of Chemistry & Biochemistry, Concordia University, Montreal, QC, Canada
| | - Teobaldo Ricardo Cuya Guizado
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ 22290-270, Brazil
- Faculty of Technology, University of the State of Rio de Janeiro, Resende, RJ 27.537-000, Brazil
| | - Pat Forgione
- Department of Chemistry & Biochemistry, Concordia University, Montreal, QC, Canada
| | - Teodorico Castro Ramalho
- Laboratory of Molecular Modeling, Chemistry Department, Federal University of Lavras, Lavras, MG, Brazil
- Faculty of Informatics and Management, Center for Basic and Applied Research, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Tanos Celmar Costa França
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ 22290-270, Brazil
- Department of Chemistry & Biochemistry, Concordia University, Montreal, QC, Canada
- Faculty of Informatics and Management, Center for Basic and Applied Research, University of Hradec Kralove, Hradec Kralove, Czech Republic
| |
Collapse
|
5
|
Mokmak W, Chunsrivirot S, Hannongbua S, Yuthavong Y, Tongsima S, Kamchonwongpaisan S. Molecular dynamics of interactions between rigid and flexible antifolates and dihydrofolate reductase from pyrimethamine-sensitive and pyrimethamine-resistant Plasmodium falciparum. Chem Biol Drug Des 2014; 84:450-61. [PMID: 24716467 DOI: 10.1111/cbdd.12334] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 03/04/2014] [Accepted: 04/03/2014] [Indexed: 01/16/2023]
Abstract
Currently, the usefulness of antimalarials such as pyrimethamine (PYR) is drastically reduced due to the emergence of resistant Plasmodium falciparum (Pf) caused by its dihydrofolate reductase (PfDHFR) mutations, especially the quadruple N51I/C59R/S108N/I164L mutations. The resistance was due to the steric conflict of PYR with S108N. WR99210 (WR), a dihydrotriazine antifolate with a flexible side chain that can avoid such conflict, can overcome this resistance through tight binding with the mutant. To understand factors contributing to different binding affinities of PYR/WR to the wild type (WT) and quadruple mutant (QM), we performed simulations on WR-WT, WR-QM, PYR-WT, and PYR-QM complexes and found that Ile14 and Asp54 were crucial for PYR/WR binding to PfDHFR due to strong hydrogen bonds. The quadruple mutations cause PYR to form, on average, fewer hydrogen bonds with Ile14 and Leu164, and to be displaced from its optimal orientation for Asp54 interaction. The predicted binding affinity ranking (WR-QM ≈ WR-WT ≈ PYR-WT >> PYR-QM) reasonably agrees with the inhibition constant (K(i)) ranking. Our results reveal important residues for tight binding of PYR/WR to WT/QM, which may be used to evaluate the inhibition effectiveness of antimalarials and to provide fundamental information for designing new drugs effective against drug-resistant P. falciparum.
Collapse
Affiliation(s)
- Wanwimon Mokmak
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Klong Luang, Pathum Thani, 12120, Thailand
| | | | | | | | | | | |
Collapse
|
6
|
Gadhe CG, Kothandan G, Cho SJ. Computational modeling of human coreceptor CCR5 antagonist as a HIV-1 entry inhibitor: using an integrated homology modeling, docking, and membrane molecular dynamics simulation analysis approach. J Biomol Struct Dyn 2013; 31:1251-76. [DOI: 10.1080/07391102.2012.732342] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
7
|
Insight into the molecular mechanism about lowered dihydrofolate binding affinity to dihydrofolate reductase-like 1 (DHFRL1). J Mol Model 2013; 19:5187-98. [PMID: 24122410 DOI: 10.1007/s00894-013-2018-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/15/2013] [Indexed: 10/26/2022]
Abstract
Human dihydrofolate reductase-like 1 (DHFRL1) has been identified as a second human dihydrofolate reductase (DHFR) enzyme. Although DHFRL1 have high sequence homology with human DHFR, dihydrofolate (DHF) exhibits a lowered binding affinity to DHFRL1 and the corresponding molecular mechanism is still unknown. To address this question, we studied the binding of DHF to DHFRL1 and DHFR by using molecular dynamics simulation. Moreover, to investigate the role the 24th residue of DHFR/DHFRL1 plays in DHF binding, R24W DHFRL1 mutant was also studied. The van der Waals interaction are more crucial for the total DHF binding energies, while the difference between the DHF binding energies of human DHFR and DHFRL1 can be attributed to the electrostatic interaction and the polar desolvation free energy.More specifically, lower DHF affinity to DHFRL1 can be mainly attributed to the reduction of net electrostatic interactions of residues Arg32 and Gln35 of DHFRL1 with DHF as being affected by Arg24. The side chain of Arg24 in DHFRL1 can extend deeply into the binding sites of DHF and NADPH, and disturb the DHF binding by steric effect, which rarely happens in human DHFR and R24W DHFRL1 mutant. Additionally, the conformation of loop I in DHFRL1 was also studied in this work. Interestingly, the loop conformation resemble to normal closed state of Escherichia coli DHFR other than the closed state of human DHFR. We hope this work will be useful to understand the general characteristics of DHFRL1.
Collapse
|
8
|
Tosso RD, Andujar SA, Gutierrez L, Angelina E, Rodríguez R, Nogueras M, Baldoni H, Suvire FD, Cobo J, Enriz RD. Molecular modeling study of dihydrofolate reductase inhibitors. Molecular dynamics simulations, quantum mechanical calculations, and experimental corroboration. J Chem Inf Model 2013; 53:2018-32. [PMID: 23834278 DOI: 10.1021/ci400178h] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A molecular modeling study on dihydrofolate reductase (DHFR) inhibitors was carried out. By combining molecular dynamics simulations with semiempirical (PM6), ab initio, and density functional theory (DFT) calculations, a simple and generally applicable procedure to evaluate the binding energies of DHFR inhibitors interacting with the human enzyme is reported here, providing a clear picture of the binding interactions of these ligands from both structural and energetic viewpoints. A reduced model for the binding pocket was used. This approach allows us to perform more accurate quantum mechanical calculations as well as to obtain a detailed electronic analysis using the quantum theory of atoms in molecules (QTAIM) technique. Thus, molecular aspects of the binding interactions between inhibitors and the DHFR are discussed in detail. A significant correlation between binding energies obtained from DFT calculations and experimental IC₅₀ values was obtained, predicting with an acceptable qualitative accuracy the potential inhibitor effect of nonsynthesized compounds. Such correlation was experimentally corroborated synthesizing and testing two new inhibitors reported in this paper.
Collapse
Affiliation(s)
- Rodrigo D Tosso
- Departamento de Química, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina
| | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
ITP Adjuster 1.0: A New Utility Program to Adjust Charges in the Topology Files Generated by the PRODRG Server. J CHEM-NY 2013. [DOI: 10.1155/2013/803151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The suitable computation of accurate atomic charges for the GROMACS topology *.itp files of small molecules, generated in the PRODRG server, has been a tricky task nowadays because it does not calculate atomic charges using an ab initio method. Usually additional steps of structure optimization and charges calculation, followed by a tedious manual replacement of atomic charges in the *.itp file, are needed. In order to assist this task, we report here the ITP Adjuster 1.0, a utility program developed to perform the replacement of the PRODRG charges in the *.itp files of small molecules by ab initio charges.
Collapse
|
10
|
Ruback E, Lobo LA, França TCC, Pascutti PG. Structural analysis of Pla protein from the biological warfare agent Yersinia pestis: docking and molecular dynamics of interactions with the mammalian plasminogen system. J Biomol Struct Dyn 2012; 31:477-84. [PMID: 22881127 DOI: 10.1080/07391102.2012.703072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Yersinia pestis protein Pla is a plasmid-coded outer membrane protein with aspartic-protease activity. Pla exhibits a plasminogen (Plg) activator activity (PAA) that promotes the cleavage of Plg to the active serine-protease form called plasmin. Exactly how Pla activates Plg into plasmin remains unclear. To investigate this event, we performed the interactions between the predicted Plg and Pla protein structures by rigid-body docking with the HEX program and evaluated the complex stability by molecular dynamics (MD) using the GROMACS package programs. The predicted docked complex of Plg-Pla shows the same interaction site predicted by experimental site-direct mutagenesis in other studies. After a total of 8 ns of MD simulation, we observed the relaxation of the beta-barrel structure of Pla and the progressive approximation and stabilization between the cleavage site of Plg into the extracellular loops of Pla, followed by the increase in the number of H bonds. We also report here the aminoacids that participate in the active site and the sub sites of interaction. The total understanding of these interactions can be an important tool for drug design against bacterial proteases.
Collapse
Affiliation(s)
- Eduardo Ruback
- Laboratory of Molecular Modeling and Dynamics , Biophysics Institute Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | | | | | | |
Collapse
|
11
|
Majumder R, Roy S, Thakur AR. Analysis of Delta–Notch interaction by molecular modeling and molecular dynamic simulation studies. J Biomol Struct Dyn 2012; 30:13-29. [DOI: 10.1080/07391102.2012.674184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|