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Zaidi NJ, Abdullah AA, Heh CH, Lin CH, Othman R, Ahmad Fuaad AAH. Hit-to-Lead Short Peptides against Dengue Type 2 Envelope Protein: Computational and Experimental Investigations. Molecules 2022; 27:molecules27103233. [PMID: 35630712 PMCID: PMC9146555 DOI: 10.3390/molecules27103233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 11/16/2022] Open
Abstract
Data from the World Health Organisation show that the global incidence of dengue infection has risen drastically, with an estimated 400 million cases of dengue infection occurring annually. Despite this worrying trend, there is still no therapeutic treatment available. Herein, we investigated short peptide fragments with a varying total number of amino acid residues (peptide fragments) from previously reported dengue virus type 2 (DENV2) peptide-based inhibitors, DN58wt (GDSYIIIGVEPGQLKENWFKKGSSIGQMF), DN58opt (TWWCFYFCRRHHPFWFFYRHN), DS36wt (LITVNPIVTEKDSPVNIEAE), and DS36opt (RHWEQFYFRRRERKFWLFFW), aided by in silico approaches: peptide–protein molecular docking and 100 ns of molecular dynamics (MD) simulation via molecular mechanics using Poisson–Boltzmann surface area (MMPBSA) and molecular mechanics generalised Born surface area (MMGBSA) methods. A library of 11,699 peptide fragments was generated, subjected to in silico calculation, and the candidates with the excellent binding affinity and shown to be stable in the DI-DIII binding pocket of DENV2 envelope (E) protein were determined. Selected peptides were synthesised using conventional Fmoc solid-phase peptide chemistry, purified by RP-HPLC, and characterised using LCMS. In vitro studies followed, to test for the peptides’ toxicity and efficacy in inhibiting the DENV2 growth cycle. Our studies identified the electrostatic interaction (from free energy calculation) to be the driving stabilising force for the E protein–peptide interactions. Five key E protein residues were also identified that had the most interactions with the peptides: (polar) LYS36, ASN37, and ARG350, and (nonpolar) LEU351 and VAL354; these residues might play crucial roles in the effective binding interactions. One of the peptide fragments, DN58opt_8-13 (PFWFFYRH), showed the best inhibitory activity, at about 63% DENV2 plague reduction, compared with no treatment. This correlates well with the in silico studies in which the peptide possessed the lowest binding energy (−9.0 kcal/mol) and was maintained steadily within the binding pocket of DENV2 E protein during the MD simulations. This study demonstrates the use of computational studies to expand research on lead optimisation of antiviral peptides, thus explaining the inhibitory potential of the designed peptides.
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Affiliation(s)
- Norburhanuddin Johari Zaidi
- Peptide Laboratory, Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
- Drug Design & Development Research Group, Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.A.A.); (C.H.H.)
| | - Adib Afandi Abdullah
- Drug Design & Development Research Group, Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.A.A.); (C.H.H.)
- Centre for Natural Products Research and Drug Discovery (CENAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Choon Han Heh
- Drug Design & Development Research Group, Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.A.A.); (C.H.H.)
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Chun-Hung Lin
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan;
| | - Rozana Othman
- Drug Design & Development Research Group, Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.A.A.); (C.H.H.)
- Centre for Natural Products Research and Drug Discovery (CENAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence: (R.O.); (A.A.H.A.F.); Tel.: +603-79674909 (R.O.); +603-79677022 (ext. 2535) (A.A.H.A.F.)
| | - Abdullah Al Hadi Ahmad Fuaad
- Peptide Laboratory, Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
- Drug Design & Development Research Group, Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.A.A.); (C.H.H.)
- Correspondence: (R.O.); (A.A.H.A.F.); Tel.: +603-79674909 (R.O.); +603-79677022 (ext. 2535) (A.A.H.A.F.)
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Amir-Hassan A, Lee VS, Baharuddin A, Othman S, Xu Y, Huang M, Yusof R, Rahman NA, Othman R. Conformational and energy evaluations of novel peptides binding to dengue virus envelope protein. J Mol Graph Model 2017; 74:273-287. [PMID: 28458006 DOI: 10.1016/j.jmgm.2017.03.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 12/13/2022]
Abstract
Effective novel peptide inhibitors which targeted the domain III of the dengue envelope (E) protein by blocking dengue virus (DENV) entry into target cells, were identified. The binding affinities of these peptides towards E-protein were evaluated by using a combination of docking and explicit solvent molecular dynamics (MD) simulation methods. The interactions of these complexes were further investigated by using the Molecular Mechanics-Poisson Boltzmann Surface Area (MMPBSA) and Molecular Mechanics Generalized Born Surface Area (MMGBSA) methods. Free energy calculations of the peptides interacting with the E-protein demonstrated that van der Waals (vdW) and electrostatic interactions were the main driving forces stabilizing the complexes. Interestingly, calculated binding free energies showed good agreement with the experimental dissociation constant (Kd) values. Our results also demonstrated that specific residues might play a crucial role in the effective binding interactions. Thus, this study has demonstrated that a combination of docking and molecular dynamics simulations can accelerate the identification process of peptides as potential inhibitors of dengue virus entry into host cells.
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Affiliation(s)
- Asfarina Amir-Hassan
- Drug Design & Development Research Group, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Pharmacy, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Vannajan Sanghiran Lee
- Drug Design & Development Research Group, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Aida Baharuddin
- Drug Design & Development Research Group, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Shatrah Othman
- Drug Design & Development Research Group, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yongtao Xu
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Northern Ireland, United Kingdom; School of Biomedical Engineering, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Meilan Huang
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Northern Ireland, United Kingdom
| | - Rohana Yusof
- Drug Design & Development Research Group, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Noorsaadah Abd Rahman
- Drug Design & Development Research Group, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Rozana Othman
- Drug Design & Development Research Group, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Pharmacy, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia; Centre for Natural Product Research and Drug Discovery, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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