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Marković V, Szczepańska A, Berlicki Ł. Antiviral Protein-Protein Interaction Inhibitors. J Med Chem 2024; 67:3205-3231. [PMID: 38394369 PMCID: PMC10945500 DOI: 10.1021/acs.jmedchem.3c01543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 01/04/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024]
Abstract
Continually repeating outbreaks of pathogenic viruses necessitate the construction of effective antiviral strategies. Therefore, the development of new specific antiviral drugs in a well-established and efficient manner is crucial. Taking into account the strong ability of viruses to change, therapies with diversified molecular targets must be sought. In addition to the widely explored viral enzyme inhibitor approach, inhibition of protein-protein interactions is a very valuable strategy. In this Perspective, protein-protein interaction inhibitors targeting HIV, SARS-CoV-2, HCV, Ebola, Dengue, and Chikungunya viruses are reviewed and discussed. Antibodies, peptides/peptidomimetics, and small molecules constitute three classes of compounds that have been explored, and each of them has some advantages and disadvantages for drug development.
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Affiliation(s)
- Violeta Marković
- Wrocław
University of Science and Technology, Department
of Bioorganic Chemistry, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
- University
of Kragujevac, Faculty of Science,
Department of Chemistry, R. Domanovića 12, 34000 Kragujevac, Serbia
| | - Anna Szczepańska
- Wrocław
University of Science and Technology, Department
of Bioorganic Chemistry, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Łukasz Berlicki
- Wrocław
University of Science and Technology, Department
of Bioorganic Chemistry, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
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2
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Lee MF, Anasir MI, Poh CL. Serum Stabilities and Antiviral Activities of Chemically Modified Peptides Against Dengue Serotypes 1-4. J Pharm Sci 2024; 113:587-595. [PMID: 38103687 DOI: 10.1016/j.xphs.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/09/2023] [Accepted: 12/09/2023] [Indexed: 12/19/2023]
Abstract
Dengue presents a major public health concern in over 100 countries due to the absence of an effective vaccine and antiviral therapy against all four dengue virus (DENV) serotypes. Several antiviral peptides were previously reported to inhibit at least three or all four DENV serotypes. Chemical modifications such as d-amino acid substitutions, polyethylene glycol (PEG)ylation, and cyclization could be applied to peptides to improve their biological activities and stability in serum. The PEGylated peptide 3 (PEG-P3) was identified to be the most promising antiviral candidate as it demonstrated good inhibitory effects against all four DENV serotypes during the pre- and post-infection stages, Based on the RP-HPLC and LC/MS analysis, peptide 4 was identified to be more stable in human serum than peptide 3, with 78.9 % and 41.6 % of the peptides remaining after 72 h of incubation in human serum, respectively. Both peptides were also able to retain their antiviral activities against specific DENV serotypes after 72 h incubation in human serum. PEG-P3 was found to be more stable than the unmodified peptide 3 with 89.4 % of PEG-P3 remaining in the human serum after 72 h of incubation. PEG-P3 was able to retain its inhibitory effects against DENV-1 to 4 after 72 h of incubation in human serum. This study provided insights into the antiviral activities and stabilities of the unmodified and chemically modified peptides in human serum.
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Affiliation(s)
- Michelle Felicia Lee
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, 5, Jalan Universiti, Bandar Sunway, Selangor 47500, Malaysia
| | - Mohd Ishtiaq Anasir
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Setia Alam, Shah Alam, Selangor Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, 5, Jalan Universiti, Bandar Sunway, Selangor 47500, Malaysia.
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3
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Akram M, Hameed S, Hassan A, Khan KM. Development in the Inhibition of Dengue Proteases as Drug Targets. Curr Med Chem 2024; 31:2195-2233. [PMID: 37723635 DOI: 10.2174/0929867331666230918110144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/24/2023] [Accepted: 08/04/2023] [Indexed: 09/20/2023]
Abstract
BACKGROUND Viral infections continue to increase morbidity and mortality severely. The flavivirus genus has fifty different species, including the dengue, Zika, and West Nile viruses that can infect 40% of individuals globally, who reside in at least a hundred different countries. Dengue, one of the oldest and most dangerous human infections, was initially documented by the Chinese Medical Encyclopedia in the Jin period. It was referred to as "water poison," connected to flying insects, i.e., Aedes aegypti and Aedes albopictus. DENV causes some medical expressions like dengue hemorrhagic fever, acute febrile illness, and dengue shock syndrome. OBJECTIVE According to the World Health Organization report of 2012, 2500 million people are in danger of contracting dengue fever worldwide. According to a recent study, 96 million of the 390 million dengue infections yearly show some clinical or subclinical severity. There is no antiviral drug or vaccine to treat this severe infection. It can be controlled by getting enough rest, drinking plenty of water, and using painkillers. The first dengue vaccine created by Sanofi, called Dengvaxia, was previously approved by the USFDA in 2019. All four serotypes of the DENV1-4 have shown re-infection in vaccine recipients. However, the usage of Dengvaxia has been constrained by its adverse effects. CONCLUSION Different classes of compounds have been reported against DENV, such as nitrogen-containing heterocycles (i.e., imidazole, pyridine, triazoles quinazolines, quinoline, and indole), oxygen-containing heterocycles (i.e., coumarins), and some are mixed heterocyclic compounds of S, N (thiazole, benzothiazine, and thiazolidinediones), and N, O (i.e., oxadiazole). There have been reports of computationally designed compounds to impede the molecular functions of specific structural and non-structural proteins as potential therapeutic targets. This review summarized the current progress in developing dengue protease inhibitors.
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Affiliation(s)
- Muhammad Akram
- Department of Chemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Shehryar Hameed
- H.E.J. Research Institute of Chemistry, International Centre for Chemical and Biological Sciences, University of Karachi, Karachi, 75720, Pakistan
| | - Abbas Hassan
- Department of Chemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Khalid Mohammed Khan
- H.E.J. Research Institute of Chemistry, International Centre for Chemical and Biological Sciences, University of Karachi, Karachi, 75720, Pakistan
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4
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Guntamadugu R, Ramakrishnan R, Darala G, Kothandan S. Molecular docking, simulations of animal peptides against the envelope protein of Dengue virus. J Biomol Struct Dyn 2023:1-15. [PMID: 37929876 DOI: 10.1080/07391102.2023.2275183] [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: 06/23/2023] [Accepted: 10/20/2023] [Indexed: 11/07/2023]
Abstract
Peptides are biologically active, small molecules with high specificity in its mode of action that can be effective at nanomolar concentrations. Peptide-based antiviral medicines have already been licensed and used to treat human immunodeficiency virus (HIV), influenza virus and hepatitis C virus. So far, no peptide drug has been approved for antiviral treatment against Dengue virus, and many are under clinical trials. Therefore, developing a reasonable peptide against the Dengue virus Envelope protein structure will be a successful strategy for treating Dengue. Hence, we investigated protein-protein docking interactions between 215 peptides retrieved from the AVP database against the envelope protein using Cluspro and HADDOCK followed by the evaluation of their allegenicity, toxicity and physicochemical characteristics investigation. Further validation of the protein-peptide complexes was performed with Molecular dynamics simulations and Molecular Mechanics Poisson-Boltzmann surface area (MMPBSA) analysis on the hit inhibitors. This study revealed that Indolicidin (-75.026 ± 1.54 KJ/mol) and Human Neutrophil peptide-1 (-71.6551 ± 2.112 KJ/mol) shows higher negative ΔG binding implicating their relative stabilization in the protein-peptide interactions during 100 ns of dynamic simulations. Also, both the peptides exhibited desirable physicochemical properties and were nonallergenic. Hence, we further aim to test these peptides by in vitro and in vivo studies to confirm their efficacy against Dengue virus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Reena Guntamadugu
- Department of Biotechnology, Saveetha School of Engineering, SIMATS, Thandalam, Tamil Nadu, India
| | - Ranjani Ramakrishnan
- Department of Virology, Sri Venkateswara University, Tirupathi, Andhra Pradesh, India
| | - Gowtham Darala
- Department of Computer Science, College of Engineering, Sri Venkateswara University, Tirupathi, Andhra Pradesh, India
| | - Sangeetha Kothandan
- Department of Biotechnology, Saveetha School of Engineering, SIMATS, Thandalam, Tamil Nadu, India
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5
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Urmi UL, Vijay AK, Kuppusamy R, Islam S, Willcox MDP. A Review of the Antiviral Activity of Cationic Antimicrobial Peptides. Peptides 2023; 166:171024. [PMID: 37172781 PMCID: PMC10170872 DOI: 10.1016/j.peptides.2023.171024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023]
Abstract
Viral epidemics are occurring frequently, and the COVID-19 viral pandemic has resulted in at least 6.5 million deaths worldwide. Although antiviral therapeutics are available, these may not have sufficient effect. The emergence of resistant or novel viruses requires new therapies. Cationic antimicrobial peptides are agents of the innate immune system that may offer a promising solution to viral infections. These peptides are gaining attention as possible therapies for viral infections or for use as prophylactic agents to prevent viral spread. This narrative review examines antiviral peptides, their structural features, and mechanism of activity. A total of 156 cationic antiviral peptides were examined for information of their mechanism of action against both enveloped and non-enveloped viruses. Antiviral peptides can be isolated from various natural sources or can be generated synthetically. The latter tend to be more specific and effective and can be made to have a broad spectrum of activity with minimal side effects. Their unique properties of being positively charges and amphipathic enable their main mode of action which is to target and disrupt viral lipid envelopes, thereby inhibiting viral entry and replication. This review offers a comprehensive summary of the current understanding of antiviral peptides, which could potentially aid in the design and creation of novel antiviral medications.
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Affiliation(s)
- Umme Laila Urmi
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Ajay Kumar Vijay
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Rajesh Kuppusamy
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia; School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Salequl Islam
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia; Department of Microbiology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh.
| | - Mark D P Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia.
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Lee MF, Wu YS, Poh CL. Molecular Mechanisms of Antiviral Agents against Dengue Virus. Viruses 2023; 15:v15030705. [PMID: 36992414 PMCID: PMC10056858 DOI: 10.3390/v15030705] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023] Open
Abstract
Dengue is a major global health threat causing 390 million dengue infections and 25,000 deaths annually. The lack of efficacy of the licensed Dengvaxia vaccine and the absence of a clinically approved antiviral against dengue virus (DENV) drive the urgent demand for the development of novel anti-DENV therapeutics. Various antiviral agents have been developed and investigated for their anti-DENV activities. This review discusses the mechanisms of action employed by various antiviral agents against DENV. The development of host-directed antivirals targeting host receptors and direct-acting antivirals targeting DENV structural and non-structural proteins are reviewed. In addition, the development of antivirals that target different stages during post-infection such as viral replication, viral maturation, and viral assembly are reviewed. Antiviral agents designed based on these molecular mechanisms of action could lead to the discovery and development of novel anti-DENV therapeutics for the treatment of dengue infections. Evaluations of combinations of antiviral drugs with different mechanisms of action could also lead to the development of synergistic drug combinations for the treatment of dengue at any stage of the infection.
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7
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Lee MF, Anasir MI, Poh CL. Development of novel antiviral peptides against dengue serotypes 1-4. Virology 2023; 580:10-27. [PMID: 36739680 DOI: 10.1016/j.virol.2023.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/25/2023] [Accepted: 01/29/2023] [Indexed: 02/03/2023]
Abstract
Dengue infections pose a critical threat to public health worldwide. Since there are no clinically approved antiviral drugs to treat dengue infections caused by the four dengue virus (DENV) serotypes, there is an urgent need to develop effective antivirals. Peptides are promising antiviral candidates due to their specificity and non-toxic properties. The DENV envelope (E) protein was selected for the design of antiviral peptides due to its importance in receptor binding and viral fusion to the host cell membrane. Twelve novel peptides were designed to mimic regions containing critical amino acid residues of the DENV E protein required for interaction with the host. A total of four peptides were identified to exhibit potent inhibitory effects against at least three or all four DENV serotypes. Peptide 3 demonstrated all three modes of action: cell protection and inhibition of post-infection against all four DENV serotypes, whereas direct virus-inactivating effects were only observed against DENV-2, 3, and 4. Peptide 4 showed good direct virus-inactivating effects against DENV-2 (74.26%) as well as good inhibitions of DENV-1 (80.37%) and DENV-4 (72.22%) during the post-infection stage. Peptide 5 exhibited direct virus-inactivating effects against all four DENV serotypes, albeit at lower inhibition levels against DENV-1 and DENV-3. It also exhibited highly significant inhibition of DENV-4 (89.31%) during post-infection. Truncated peptide 5F which was derived from peptide 5 showed more significant inhibition of DENV-4 (91.58%) during post-infection and good direct virus-inactivating effects against DENV-2 (77.55%) at a lower concentration of 100 μM. Peptide 3 could be considered as the best antiviral candidate for pre- and post-infection treatments of DENV infections in regions with four circulating dengue serotypes. However, if the most predominant dengue serotype for a particular region could be identified, peptides with significantly high antiviral activities against that particular dengue serotype could serve as more suitable antiviral candidates. Thus, peptide 5F serves as a more suitable antiviral candidate for post-infection treatment against DENV-4.
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Affiliation(s)
- Michelle Felicia Lee
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, 5, Jalan Universiti, Bandar Sunway, Selangor, 47500, Malaysia
| | - Mohd Ishtiaq Anasir
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Setia Alam, Shah Alam, Selangor, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, 5, Jalan Universiti, Bandar Sunway, Selangor, 47500, Malaysia.
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8
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Bruggemann L, Falls Z, Mangione W, Schwartz SA, Battaglia S, Aalinkeel R, Mahajan SD, Samudrala R. Multiscale Analysis and Validation of Effective Drug Combinations Targeting Driver KRAS Mutations in Non-Small Cell Lung Cancer. Int J Mol Sci 2023; 24:ijms24020997. [PMID: 36674513 PMCID: PMC9867122 DOI: 10.3390/ijms24020997] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/04/2022] [Accepted: 11/06/2022] [Indexed: 01/06/2023] Open
Abstract
Pharmacogenomics is a rapidly growing field with the goal of providing personalized care to every patient. Previously, we developed the Computational Analysis of Novel Drug Opportunities (CANDO) platform for multiscale therapeutic discovery to screen optimal compounds for any indication/disease by performing analytics on their interactions using large protein libraries. We implemented a comprehensive precision medicine drug discovery pipeline within the CANDO platform to determine which drugs are most likely to be effective against mutant phenotypes of non-small cell lung cancer (NSCLC) based on the supposition that drugs with similar interaction profiles (or signatures) will have similar behavior and therefore show synergistic effects. CANDO predicted that osimertinib, an EGFR inhibitor, is most likely to synergize with four KRAS inhibitors.Validation studies with cellular toxicity assays confirmed that osimertinib in combination with ARS-1620, a KRAS G12C inhibitor, and BAY-293, a pan-KRAS inhibitor, showed a synergistic effect on decreasing cellular proliferation by acting on mutant KRAS. Gene expression studies revealed that MAPK expression is strongly correlated with decreased cellular proliferation following treatment with KRAS inhibitor BAY-293, but not treatment with ARS-1620 or osimertinib. These results indicate that our precision medicine pipeline may be used to identify compounds capable of synergizing with inhibitors of KRAS G12C, and to assess their likelihood of becoming drugs by understanding their behavior at the proteomic/interactomic scales.
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Affiliation(s)
- Liana Bruggemann
- Department of Biomedical Informatics, University at Buffalo, Buffalo, NY 14260, USA
| | - Zackary Falls
- Department of Biomedical Informatics, University at Buffalo, Buffalo, NY 14260, USA
| | - William Mangione
- Department of Biomedical Informatics, University at Buffalo, Buffalo, NY 14260, USA
| | | | | | | | - Supriya D. Mahajan
- Department of Medicine, University at Buffalo, Buffalo, NY 14260, USA
- Correspondence: (S.D.M.); (R.S.)
| | - Ram Samudrala
- Department of Biomedical Informatics, University at Buffalo, Buffalo, NY 14260, USA
- Correspondence: (S.D.M.); (R.S.)
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9
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Singh I, Singh S, Ojha KK, Yadav NS. Designing Self-Inhibitory fusion peptide analogous to viral spike protein against novel severe acute respiratory syndrome (SARS-CoV-2). J Biomol Struct Dyn 2022; 40:11357-11372. [PMID: 34379031 DOI: 10.1080/07391102.2021.1960192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
COVID-19 is a highly contagious viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is declared pandemic by the World Health Organization (WHO). The spike protein of SARS-CoV-2 is a key component playing a pivotal role in facilitating viral fusion as well as release of genome into the host cell. Till date there is no clinically approved vaccine or drug available against Covid-19. We designed four hydrophobic inhibitory peptides (ITPs) based on WWIHS (Wimley and White interfacial hydrophobicity scale) score, targeting the HR1 domain of spike protein. Two inhibitory peptides out of four have a strong affinity to the hydrophobic surface of HR1 domain in pre-fusion spike protein. The MD simulation result showed the strong accommodation of ITPs with HR1 domain surface. These self-inhibitory peptides mimic the function of HR2 by binding to HR1 domain, thus inhibiting the formation of HR1-HR2 post-fusion complex, which is a key structure for virus-host tropism.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Indra Singh
- School of Biotechnology, Banaras Hindu University, Varanasi, India
| | - Shalini Singh
- School of Biochemical Engineering Indian Institute of Technology, Banaras Hindu University, Varanasi, India
| | - Krishna Kumar Ojha
- Department of Bioinformatics, Central University of South Bihar, Gaya, India
| | - Neetu Singh Yadav
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, India
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10
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Proteochemometric Method for pIC50 Prediction of Flaviviridae. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7901791. [PMID: 36158882 PMCID: PMC9499780 DOI: 10.1155/2022/7901791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022]
Abstract
Viruses remain an area of concern despite constant development of antiviral drugs and therapies. One of the contributors is the Flaviviridae family of viruses causing diseases that need attention. Among other anitviral methods, antiviral peptides are being studied as viable candidates. Although antiviral peptides (AVPs) are emerging as potential therapeutics, it is important to assess the efficacy of a given peptide in terms of its bioactivity. Experimental identification of the bioactivity of each potential peptide is an expensive and time consuming task. Computational methods like proteochemometric modeling (PCM) is a promising method for prediction of bioactivity (pIC50) based on peptide and target sequence pair. In this study, we propose a prediction of pIC50 of AVP against the Flaviviridae family that may help make the decision to choose a peptide with desired efficacy. The peptides data was collected from a public database and target sequences were manually curated from literature. Features are calculated using peptide and target sequence PCM descriptors which consist of individual and cross-term features of peptide and respective target. The resultant R2 and MAPE values are 0.85 and 8.44%, respectively, for prediction of pIC50 value of AVPs.
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11
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Identification of antiviral peptide inhibitors for receptor binding domain of SARS-CoV-2 omicron and its sub-variants: an in-silico approach. 3 Biotech 2022; 12:198. [PMID: 35923684 PMCID: PMC9342843 DOI: 10.1007/s13205-022-03258-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/08/2022] [Indexed: 11/01/2022] Open
Abstract
Omicron, a variant of concern (VOC) of SARS-CoV-2, emerged in South Africa in November 2021. Omicron has been continuously acquiring a series of new mutations, especially in the spike (S) protein that led to high infectivity and transmissibility. Peptides targeting the receptor-binding domain (RBD) of the spike protein by which omicron and its variants attach to the host receptor, angiotensin-converting enzyme (ACE2) can block the viral infection at the first step. This study aims to identify antiviral peptides from the Antiviral peptide database (AVPdb) and HIV-inhibitory peptide database (HIPdb) against the RBD of omicron by using a molecular docking approach. The lead RBD binder peptides obtained through molecular docking were screened for allergenicity and physicochemical criteria (isoelectric point (pI) and net charge) required for peptide-based drugs. The binding affinity of the best five peptide inhibitors with the RBD of omicron was validated further by molecular dynamics (MD) simulation. Our result introduces five antiviral peptides, including AVP1056, AVP1059, AVP1225, AVP1801, and HIP755, that may effectively hinder omicron-host interactions. It is worth mentioning that all the three major sub-variants of omicron, BA.1 (B.1.1.529.1), BA.2 (B.1.1.529.2), and BA.3 (B.1.1.529.3), exhibits conserved ACE-2 interacting residues. Hence, the screened antiviral peptides with similar affinity can also interrupt the RBD-mediated invasion of different major sub-variants of omicron. Altogether, these peptides can be considered in the peptide-based therapeutics development for omicron treatment after further experimentation. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03258-4.
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12
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Lee YCJ, Shirkey JD, Park J, Bisht K, Cowan AJ. An Overview of Antiviral Peptides and Rational Biodesign Considerations. BIODESIGN RESEARCH 2022; 2022:9898241. [PMID: 37850133 PMCID: PMC10521750 DOI: 10.34133/2022/9898241] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/04/2022] [Indexed: 10/19/2023] Open
Abstract
Viral diseases have contributed significantly to worldwide morbidity and mortality throughout history. Despite the existence of therapeutic treatments for many viral infections, antiviral resistance and the threat posed by novel viruses highlight the need for an increased number of effective therapeutics. In addition to small molecule drugs and biologics, antimicrobial peptides (AMPs) represent an emerging class of potential antiviral therapeutics. While AMPs have traditionally been regarded in the context of their antibacterial activities, many AMPs are now known to be antiviral. These antiviral peptides (AVPs) have been shown to target and perturb viral membrane envelopes and inhibit various stages of the viral life cycle, from preattachment inhibition through viral release from infected host cells. Rational design of AMPs has also proven effective in identifying highly active and specific peptides and can aid in the discovery of lead peptides with high therapeutic selectivity. In this review, we highlight AVPs with strong antiviral activity largely curated from a publicly available AMP database. We then compile the sequences present in our AVP database to generate structural predictions of generic AVP motifs. Finally, we cover the rational design approaches available for AVPs taking into account approaches currently used for the rational design of AMPs.
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Affiliation(s)
- Ying-Chiang J. Lee
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Jaden D. Shirkey
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Jongbeom Park
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Karishma Bisht
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Alexis J. Cowan
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
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13
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Yu Y, Si L, Meng Y. Flavivirus Entry Inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1366:171-197. [PMID: 35412141 DOI: 10.1007/978-981-16-8702-0_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Flaviviruses, including Dengue virus, Zika virus, Yellow fever virus, Japanese encephalitis virus, West Nile virus, cause thousands of deaths and millions of illnesses each year. The large outbreak of ZIKV in 2016 reminds us that flaviviruses can pose a serious threat to human safety and public health as emerging and re-emerging viruses. However, there are no specific drugs approved for the treatment of flavivirus infections. Due to no need to enter the cells, viral entry inhibitors have the unique advantage in suppressing viral infections. Flaviviruses bind to receptors and attach to the cell surface, then enter the endosome in a clathrin-dependent manner and finalizes the viral entry process after fusion with the cell membrane in a low pH environment. Small molecules, antibodies or peptides can inhibit flavivirus entry by targeting the above processes. Here, we focus on flavivirus entry inhibitors with well-defined target and antiviral activity. We hope that our review will provide a theoretical basis for flavivirus treatment and drug research and help to accelerate the clinical application of flavivirus entry inhibitors.
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Affiliation(s)
- Yufeng Yu
- Medical School, Nanjing University, Nanjing, Jiangsu, China.
| | - Lulu Si
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yu Meng
- Department of Microbiology and Immunology, College of Basic Medical Sciences, Dali University, Dali, Yunnan, China
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14
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Sundar S, Piramanayagam S, Natarajan J. A review on structural genomics approach applied for drug discovery against three vector-borne viral diseases: Dengue, Chikungunya and Zika. Virus Genes 2022; 58:151-171. [PMID: 35394596 DOI: 10.1007/s11262-022-01898-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/22/2022] [Indexed: 12/22/2022]
Abstract
Structural genomics involves the advent of three-dimensional structures of the genome encoded proteins through various techniques available. Numerous structural genomics research groups have been developed across the globe and they contribute enormously to the identification of three-dimensional structures of various proteins. In this review, we have discussed the applications of the structural genomics approach towards the discovery of potential lead-like molecules against the genomic drug targets of three vector-borne diseases, namely, Dengue, Chikungunya and Zika. Currently, all these three diseases are associated with the most important global public health problems and significant economic burden in tropical countries. Structural genomics has accelerated the identification of novel drug targets and inhibitors for the treatment of these diseases. We start with the current development status of the drug targets and antiviral drugs against these three diseases and conclude by describing challenges that need to be addressed to overcome the shortcomings in the process of drug discovery.
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Affiliation(s)
- Shobana Sundar
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India
| | | | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India.
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15
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Mangione W, Falls Z, Samudrala R. Optimal COVID-19 therapeutic candidate discovery using the CANDO platform. Front Pharmacol 2022; 13:970494. [PMID: 36091793 PMCID: PMC9452636 DOI: 10.3389/fphar.2022.970494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/07/2022] [Indexed: 01/22/2023] Open
Abstract
The worldwide outbreak of SARS-CoV-2 in early 2020 caused numerous deaths and unprecedented measures to control its spread. We employed our Computational Analysis of Novel Drug Opportunities (CANDO) multiscale therapeutic discovery, repurposing, and design platform to identify small molecule inhibitors of the virus to treat its resulting indication, COVID-19. Initially, few experimental studies existed on SARS-CoV-2, so we optimized our drug candidate prediction pipelines using results from two independent high-throughput screens against prevalent human coronaviruses. Ranked lists of candidate drugs were generated using our open source cando.py software based on viral protein inhibition and proteomic interaction similarity. For the former viral protein inhibition pipeline, we computed interaction scores between all compounds in the corresponding candidate library and eighteen SARS-CoV proteins using an interaction scoring protocol with extensive parameter optimization which was then applied to the SARS-CoV-2 proteome for prediction. For the latter similarity based pipeline, we computed interaction scores between all compounds and human protein structures in our libraries then used a consensus scoring approach to identify candidates with highly similar proteomic interaction signatures to multiple known anti-coronavirus actives. We published our ranked candidate lists at the very beginning of the COVID-19 pandemic. Since then, 51 of our 276 predictions have demonstrated anti-SARS-CoV-2 activity in published clinical and experimental studies. These results illustrate the ability of our platform to rapidly respond to emergent pathogens and provide greater evidence that treating compounds in a multitarget context more accurately describes their behavior in biological systems.
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Affiliation(s)
- William Mangione
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - Zackary Falls
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - Ram Samudrala
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
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16
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Schuler J, Falls Z, Mangione W, Hudson ML, Bruggemann L, Samudrala R. Evaluating the performance of drug-repurposing technologies. Drug Discov Today 2022; 27:49-64. [PMID: 34400352 PMCID: PMC10014214 DOI: 10.1016/j.drudis.2021.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 06/20/2021] [Accepted: 08/08/2021] [Indexed: 01/22/2023]
Abstract
Drug-repurposing technologies are growing in number and maturing. However, comparisons to each other and to reality are hindered because of a lack of consensus with respect to performance evaluation. Such comparability is necessary to determine scientific merit and to ensure that only meaningful predictions from repurposing technologies carry through to further validation and eventual patient use. Here, we review and compare performance evaluation measures for these technologies using version 2 of our shotgun repurposing Computational Analysis of Novel Drug Opportunities (CANDO) platform to illustrate their benefits, drawbacks, and limitations. Understanding and using different performance evaluation metrics ensures robust cross-platform comparability, enabling us to continue to strive toward optimal repurposing by decreasing the time and cost of drug discovery and development.
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Affiliation(s)
- James Schuler
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
| | - Zackary Falls
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - William Mangione
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Matthew L Hudson
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Liana Bruggemann
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Ram Samudrala
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
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17
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Manna S, Chowdhury T, M. Mandal S, Choudhury SM. Short Amphiphiles or Micelle Peptides May Help to Fight Against
COVID-19. Curr Protein Pept Sci 2022; 23:33-43. [DOI: 10.2174/1389203723666220127154159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/29/2021] [Accepted: 11/26/2021] [Indexed: 11/22/2022]
Abstract
Background:
COVID-19 is a worldwide threat because of the incessant spread of SARS-CoV-2 which urges the development of suitable antiviral drug to secure our society. Already, a group of peptides have been recommended for SARS-CoV-2, but not yet established. SARS-CoV-2 is an enveloped virus with hydrophobic fusion protein and spike glycoproteins.
Methods:
Here, we have summarized several reported amphiphilic peptides and their in-silico docking analysis with spike glycoprotein of SARS-CoV-2.
Result:
The result revealed the complex formation of spike protein and amphiphilic peptides with higher binding affinity. It was also observed that PalL1 (ARLPRTMVHPKPAQP), 10AN1 (FWFTLIKTQAKQPARYRRFC), THETA defensin (RCICGRGICRLL) and mucroporin M1 (LFRLIKSLIKRLVSAFK) showed the binding free energy more than -1000 kcal/mol. Molecular pI and hydrophobicity are also important factors of peptides to enhance the binding affinity with spike protein of SARS-CoV-2
Conclusion:
In the light of these findings, it is necessary to check the real efficacy of amphiphilic peptides in-vitro to in-vivo experimental set up to develop an effective anti-SARS-CoV-2 peptide drug, which might help to control the current pandemic situation.
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Affiliation(s)
- Sounik Manna
- Department of Human Physiology, Vidyasagar University, Midnapore 721 102, West Bengal, India
- Department of Microbiology, Midnapore College (Autonomous), Paschim Medinipur 721101, India
| | - Trinath Chowdhury
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Santi M. Mandal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sujata Maiti Choudhury
- Department of Human Physiology, Vidyasagar University, Midnapore 721 102, West Bengal, India
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18
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Düzgüneş N, Fernandez-Fuentes N, Konopka K. Inhibition of Viral Membrane Fusion by Peptides and Approaches to Peptide Design. Pathogens 2021; 10:1599. [PMID: 34959554 PMCID: PMC8709411 DOI: 10.3390/pathogens10121599] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 12/29/2022] Open
Abstract
Fusion of lipid-enveloped viruses with the cellular plasma membrane or the endosome membrane is mediated by viral envelope proteins that undergo large conformational changes following binding to receptors. The HIV-1 fusion protein gp41 undergoes a transition into a "six-helix bundle" after binding of the surface protein gp120 to the CD4 receptor and a co-receptor. Synthetic peptides that mimic part of this structure interfere with the formation of the helix structure and inhibit membrane fusion. This approach also works with the S spike protein of SARS-CoV-2. Here we review the peptide inhibitors of membrane fusion involved in infection by influenza virus, HIV-1, MERS and SARS coronaviruses, hepatitis viruses, paramyxoviruses, flaviviruses, herpesviruses and filoviruses. We also describe recent computational methods used for the identification of peptide sequences that can interact strongly with protein interfaces, with special emphasis on SARS-CoV-2, using the PePI-Covid19 database.
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Affiliation(s)
- Nejat Düzgüneş
- Department of Biomedical Sciences, Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, CA 94103, USA;
| | - Narcis Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3EE, UK;
| | - Krystyna Konopka
- Department of Biomedical Sciences, Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, CA 94103, USA;
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19
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Overhoff B, Falls Z, Mangione W, Samudrala R. A Deep-Learning Proteomic-Scale Approach for Drug Design. Pharmaceuticals (Basel) 2021; 14:1277. [PMID: 34959678 PMCID: PMC8709297 DOI: 10.3390/ph14121277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 12/26/2022] Open
Abstract
Computational approaches have accelerated novel therapeutic discovery in recent decades. The Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun multitarget therapeutic discovery, repurposing, and design aims to improve their efficacy and safety by employing a holistic approach that computes interaction signatures between every drug/compound and a large library of non-redundant protein structures corresponding to the human proteome fold space. These signatures are compared and analyzed to determine if a given drug/compound is efficacious and safe for a given indication/disease. In this study, we used a deep learning-based autoencoder to first reduce the dimensionality of CANDO-computed drug-proteome interaction signatures. We then employed a reduced conditional variational autoencoder to generate novel drug-like compounds when given a target encoded "objective" signature. Using this approach, we designed compounds to recreate the interaction signatures for twenty approved and experimental drugs and showed that 16/20 designed compounds were predicted to be significantly (p-value ≤ 0.05) more behaviorally similar relative to all corresponding controls, and 20/20 were predicted to be more behaviorally similar relative to a random control. We further observed that redesigns of objectives developed via rational drug design performed significantly better than those derived from natural sources (p-value ≤ 0.05), suggesting that the model learned an abstraction of rational drug design. We also show that the designed compounds are structurally diverse and synthetically feasible when compared to their respective objective drugs despite consistently high predicted behavioral similarity. Finally, we generated new designs that enhanced thirteen drugs/compounds associated with non-small cell lung cancer and anti-aging properties using their predicted proteomic interaction signatures. his study represents a significant step forward in automating holistic therapeutic design with machine learning, enabling the rapid generation of novel, effective, and safe drug leads for any indication.
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Affiliation(s)
| | | | | | - Ram Samudrala
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA; (B.O.); (Z.F.); (W.M.)
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20
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Cordero-Rivera CD, De Jesús-González LA, Osuna-Ramos JF, Palacios-Rápalo SN, Farfan-Morales CN, Reyes-Ruiz JM, Del Ángel RM. The importance of viral and cellular factors on flavivirus entry. Curr Opin Virol 2021; 49:164-175. [PMID: 34171540 DOI: 10.1016/j.coviro.2021.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 12/17/2022]
Abstract
The flavivirus are emerging and re-emerging arthropod-borne pathogens responsible for significant mortality and morbidity worldwide. The genus comprises more than 70 viruses, and despite genomic and structural similarities, infections by different flaviviruses result in different clinical presentations. In the absence of a safe and effective vaccine against these infections, the search for new strategies to inhibit viral infection is necessary. The life cycle of arboviruses begins with the entry process composed of multiple steps: attachment, internalization, endosomal escape and capsid uncoating. This mini-review describes factors and mechanisms involved in the viral entry as events required to take over the cellular machinery and host factors and cellular pathways commonly used by flaviviruses as possible approaches for developing broad-spectrum antiviral drugs.
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Affiliation(s)
- Carlos Daniel Cordero-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Intituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México 07320, Mexico
| | - Luis Adrián De Jesús-González
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Intituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México 07320, Mexico
| | - Juan Fidel Osuna-Ramos
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Intituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México 07320, Mexico
| | - Selvin Noé Palacios-Rápalo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Intituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México 07320, Mexico
| | - Carlos Noe Farfan-Morales
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Intituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México 07320, Mexico
| | - José Manuel Reyes-Ruiz
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Intituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México 07320, Mexico
| | - Rosa María Del Ángel
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Intituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México 07320, Mexico.
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21
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Gallo FN, Enderle AG, Pardo LA, Leal ES, Bollini M. Challenges and perspectives in the discovery of dengue virus entry inhibitors. Curr Med Chem 2021; 29:719-740. [PMID: 34036904 DOI: 10.2174/0929867328666210521213118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 11/22/2022]
Abstract
Dengue virus (DENV) disease has become one of the major challenges in public health. Currently, there is no antiviral treatment for this infection. Since human transmission occurs via mosquitoes of the Aedes genus, most efforts have been focused on controlling this vector. However, these control strategies have not been totally successful, as reflected in the increasing number of DENV infections per year, becoming an endemic disease in more than 100 countries worldwide. Consequently, the development of a safe antiviral agent is urgently needed. In this sense, rational design approaches have been applied in the development of antiviral compounds that inhibit one or more steps in the viral replication cycle. The entry of viruses into host cells is an early and specific stage of infection. Targeting either viral components or cellular protein targets is an affordable and effective strategy for therapeutic intervention of viral infections. This review provides an extensive overview of the small organic molecules, peptides, and inorganic moieties that have been tested so far as DENV entry direct-acting antiviral agents. The latest advances based on computer-aided drug design (CADD) strategies and traditional medicinal chemistry approaches in the design and evaluation of DENV virus entry inhibitors will be discussed. Furthermore, physicochemical drug properties such as solubility, lipophilicity, stability, and current results of pre-clinical and clinical studies will also be discussed in detail.
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Affiliation(s)
- Facundo N Gallo
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz, 2390, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ana G Enderle
- Laboratorio de Desarrollo Analítico y Quimiometría (LADAQ), Cátedra de Química Analítica I, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral-CONICET, Ciudad Universitaria, 3000, Santa Fe, Argentina
| | - Lucas A Pardo
- Department of Bioengineering, McGill University, 3480 University Street, Montreal, Canada
| | - Emilse S Leal
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz, 2390, Ciudad Autónoma de Buenos Aires, Argentina
| | - Mariela Bollini
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz, 2390, Ciudad Autónoma de Buenos Aires, Argentina
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22
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S AH, Pujar GV, Sethu AK, Bhagyalalitha M, Singh M. Dengue structural proteins as antiviral drug targets: Current status in the drug discovery & development. Eur J Med Chem 2021; 221:113527. [PMID: 34020338 DOI: 10.1016/j.ejmech.2021.113527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/30/2021] [Accepted: 04/20/2021] [Indexed: 01/04/2023]
Abstract
Dengue virus belongs to the class of RNA viruses and subclass of enveloped single-stranded positive-sense RNA virus. It causes dengue fever (DF), dengue hemorrhagic fever (DHF), or dengue shock syndrome (DSS), where DHF and DSS are life-threatening. Even though dengue is an age-old disease, it is still a mystery and continues to be a global threat. Numerous attempts have been carried out in the past few decades to eradicate the virus through vaccine and antiviral drugs, but still battle continues. In this review, the possible drug targets for discovery and development of potential antiviral drugs against structural proteins of dengue virus, the current development status of the antiviral drugs against dengue around the world, and challenges that need to be addressed to overcome the shortcomings in the process of drug discovery have been discussed.
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Affiliation(s)
- Akshatha H S
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
| | - Gurubasavaraj V Pujar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India.
| | - Arun Kumar Sethu
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
| | - Meduri Bhagyalalitha
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
| | - Manisha Singh
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Sri Shivarathreeshwara Nagara, Mysuru, 570015, India
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23
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Arumugam AC, Agharbaoui FE, Khazali AS, Yusof R, Abd Rahman N, Ahmad Fuaad AAH. Computational-aided design: minimal peptide sequence to block dengue virus transmission into cells. J Biomol Struct Dyn 2020; 40:5026-5035. [PMID: 33382015 DOI: 10.1080/07391102.2020.1866074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dengue virus (DV) infection is one of the main public health concerns, affecting approximately 390 million people worldwide, as reported by the World Health Organization. Yet, there is no antiviral treatment for DV infection. Therefore, the development of potent and nontoxic anti-DV, as a complement for the existing treatment strategies, is urgently needed. Herein, we investigate a series of small peptides inhibitors of DV antiviral activity targeting the entry process as the promising strategy to block DV infection. The peptides were designed based on our previously reported peptide sequence, DN58opt (TWWCFYFCRRHHPFWFFYRHN), to identify minimal effective inhibitory sequence through molecular docking and dynamics studies. The in silico designed peptides were synthesized using conventional Fmoc solid-phase peptide synthesis chemistry, purified by RP-HPLC and characterized using LCMS. Later, they were screened for their antiviral activity. One of the peptides, AC 001, was able to reduce about 40% of DV plaque formation. This observation correlates well with the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) analysis - AC 001 showed the most favorable binding affinity through 60 ns simulations. Pairwise residue decomposition analysis has revealed four key residues that contributed to the binding of these peptides into the DV2 E protein pocket. This work identifies the minimal peptide sequence required to inhibit DV replication and explains the behavior observed on an atomic level using computational study.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aathe Cangaree Arumugam
- Faculty of Science, Department of Chemistry, DDDRG, Universiti Malaya, Kuala Lumpur, Malaysia
| | | | - Ahmad Suhail Khazali
- Faculty of Medicine, Department of Molecular Medicine, Universiti Malaya, Kuala Lumpur, Malaysia.,Faculty of Applied Sciences, Universiti Teknologi Mara, Arau, Perlis, Malaysia
| | - Rohana Yusof
- Faculty of Medicine, Department of Molecular Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Noorsaadah Abd Rahman
- Faculty of Science, Department of Chemistry, DDDRG, Universiti Malaya, Kuala Lumpur, Malaysia
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24
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Troost B, Smit JM. Recent advances in antiviral drug development towards dengue virus. Curr Opin Virol 2020; 43:9-21. [PMID: 32795907 DOI: 10.1016/j.coviro.2020.07.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/09/2020] [Indexed: 01/29/2023]
Abstract
Despite the high disease burden of dengue virus, there is no approved antiviral treatment or broadly applicable vaccine to treat or prevent dengue virus infection. In the last decade, many antiviral compounds have been identified but only few have been further evaluated in pre-clinical or clinical trials. This review will give an overview of the direct-acting and host-directed antivirals identified to date. Furthermore, important parameters for further development that is, drug properties including efficacy, specificity and stability, pre-clinical animal testing, and combinational drug therapy will be discussed.
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Affiliation(s)
- Berit Troost
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jolanda M Smit
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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25
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Shanmugam A, Ramakrishnan C, Velmurugan D, Gromiha MM. Identification of Potential Inhibitors for Targets Involved in Dengue Fever. Curr Top Med Chem 2020; 20:1742-1760. [PMID: 32552652 DOI: 10.2174/1568026620666200618123026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/05/2019] [Accepted: 01/10/2020] [Indexed: 01/16/2023]
Abstract
Lethality due to dengue infection is a global threat. Nearly 400 million people are affected every year, which approximately costs 500 million dollars for surveillance and vector control itself. Many investigations on the structure-function relationship of proteins expressed by the dengue virus are being made for more than a decade and had come up with many reports on small molecule drug discovery. In this review, we present a detailed note on viral proteins and their functions as well as the inhibitors discovered/designed so far using experimental and computational methods. Further, the phytoconstituents from medicinal plants, specifically the extract of the papaya leaves, neem and bael, which combat dengue infection via dengue protease, helicase, methyl transferase and polymerase are summarized.
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Affiliation(s)
- Anusuya Shanmugam
- Department of Pharmaceutical Engineering, Vinayaka Mission's Kirupananda Variyar Engineering College, Vinayaka Mission's Research Foundation (Deemed to be University), Salem - 636308, India
| | - Chandrasekaran Ramakrishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai - 600036, India
| | - Devadasan Velmurugan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai - 600025, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai - 600036, India
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26
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Su X, Wang Q, Wen Y, Jiang S, Lu L. Protein- and Peptide-Based Virus Inactivators: Inactivating Viruses Before Their Entry Into Cells. Front Microbiol 2020; 11:1063. [PMID: 32523582 PMCID: PMC7261908 DOI: 10.3389/fmicb.2020.01063] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 04/29/2020] [Indexed: 12/20/2022] Open
Abstract
Infectious diseases caused by human immunodeficiency virus (HIV) and other highly pathogenic enveloped viruses, have threatened the global public health. Most antiviral drugs act as passive defenders to inhibit viral replication inside the cell, while a few of them function as gate keepers to combat viruses outside the cell, including fusion inhibitors, e.g., enfuvirtide, and receptor antagonists, e.g., maraviroc, as well as virus inactivators (including attachment inhibitors). Different from fusion inhibitors and receptor antagonists that must act in the presence of target cells, virus inactivators can actively inactivate cell-free virions in the blood, through interaction with one or more sites in the envelope glycoproteins (Envs) on virions. Notably, a number of protein- and peptide-based virus inactivators (PPVIs) under development are expected to have a better utilization rate than the current antiviral drugs and be safer for in vivo human application than the chemical-based virus inactivators. Here we have highlighted recent progress in developing PPVIs against several important enveloped viruses, including HIV, influenza virus, Zika virus (ZIKV), dengue virus (DENV), and herpes simplex virus (HSV), and the potential use of PPVIs for urgent treatment of infection by newly emerging or re-emerging viruses.
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Affiliation(s)
- Xiaojie Su
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qian Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yumei Wen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China.,Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, United States
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China
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Zhao D, Zhang L, Han K, Liu Q, Yang J, Huang X, Liu Y, Li Y, Zhao P. Peptide inhibitors of tembusu virus infection derived from the envelope protein. Vet Microbiol 2020; 245:108708. [PMID: 32456819 PMCID: PMC7204726 DOI: 10.1016/j.vetmic.2020.108708] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/21/2020] [Accepted: 04/25/2020] [Indexed: 01/30/2023]
Abstract
The outbreak and spread of Tembusu virus (TMUV) has caused very large losses in the waterfowl-breeding industry since 2010. The viral envelope (E) protein, the principal surface protein of viral particles, plays a vital role in viral entry and fusion. In this study, two peptides derived from domain II (DII) and the stem of the TMUV envelope protein, TP1 and TP2, respectively, were tested for their antiviral activity. TP1 and TP2 inhibited TMUV infection in BHK-21 cells, and their 50% inhibitory concentrations (IC50) were 14.19 mg/L and 7.64 mg/L, respectively. Viral inhibition assays in different cell lines of avian origin showed that the inhibitory effects of TP1 and TP2 are not cell type dependent. Moreover, TP2 also exhibited inhibitory activity against Japanese encephalitis virus (JEV) infection. The two peptides inhibited antibody-mediated TMUV infection of duck peripheral blood lymphocytes. Co-immunoprecipitation assays and indirect enzyme-linked immunosorbent assays (ELISAs) indicated that both peptides interact with the surface of the TMUV virion. RNase digestion assays confirmed the release of viral RNA following incubation with TP1, while incubation with TP1 or TP2 interfered with the binding between TMUV and cells. Taken together, these results show that TP1 and TP2 may be developed into antiviral treatments against TMUV infection.
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Affiliation(s)
- Dongmin Zhao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Province, PR China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, Jiangsu Province, PR China
| | - Lijiao Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Province, PR China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, Jiangsu Province, PR China
| | - Kaikai Han
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Province, PR China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, Jiangsu Province, PR China
| | - Qingtao Liu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Province, PR China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, Jiangsu Province, PR China
| | - Jing Yang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Province, PR China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, Jiangsu Province, PR China
| | - Xinmei Huang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Province, PR China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, Jiangsu Province, PR China
| | - Yuzhuo Liu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Province, PR China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, Jiangsu Province, PR China
| | - Yin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Jiangsu Province, PR China; Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, Jiangsu Province, PR China.
| | - Peng Zhao
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong province, PR China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Tai'an, Shandong, PR China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Tai'an, Shandong, PR China.
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Anasir MI, Ramanathan B, Poh CL. Structure-Based Design of Antivirals against Envelope Glycoprotein of Dengue Virus. Viruses 2020; 12:v12040367. [PMID: 32225021 PMCID: PMC7232406 DOI: 10.3390/v12040367] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 02/06/2023] Open
Abstract
Dengue virus (DENV) presents a significant threat to global public health with more than 500,000 hospitalizations and 25,000 deaths annually. Currently, there is no clinically approved antiviral drug to treat DENV infection. The envelope (E) glycoprotein of DENV is a promising target for drug discovery as the E protein is important for viral attachment and fusion. Understanding the structure and function of DENV E protein has led to the exploration of structure-based drug discovery of antiviral compounds and peptides against DENV infections. This review summarizes the structural information of the DENV E protein with regards to DENV attachment and fusion. The information enables the development of antiviral agents through structure-based approaches. In addition, this review compares the potency of antivirals targeting the E protein with the antivirals targeting DENV multifunctional enzymes, repurposed drugs and clinically approved antiviral drugs. None of the current DENV antiviral candidates possess potency similar to the approved antiviral drugs which indicates that more efforts and resources must be invested before an effective DENV drug materializes.
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Affiliation(s)
- Mohd Ishtiaq Anasir
- Center for Virus and Vaccine Research, School of Science and Technology, Sunway University, Kuala Lumpur, Selangor 47500, Malaysia;
| | - Babu Ramanathan
- Department of Biological Sciences, School of Science and Technology, Sunway University, Kuala Lumpur, Selangor 47500, Malaysia;
| | - Chit Laa Poh
- Center for Virus and Vaccine Research, School of Science and Technology, Sunway University, Kuala Lumpur, Selangor 47500, Malaysia;
- Correspondence: ; Tel.: +60-3-7491-8622; Fax: +60-3-5635-8633
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Barr KL, Schwarz ER, Prakoso D, Imtiaz K, Pu R, Morris JG, Khan E, Long MT. Strain-Dependent Activity of Zika Virus and Exposure History in Serological Diagnostics. Trop Med Infect Dis 2020; 5:tropicalmed5010038. [PMID: 32138262 PMCID: PMC7157670 DOI: 10.3390/tropicalmed5010038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/13/2020] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
Zika virus (ZIKV) circulates as two separate lineages, with significant genetic variability between strains. Strain-dependent activity has been reported for dengue virus, herpes simplex virus and influenza. Strain-dependent activity of subject specimens to a virus could be an impediment to serological diagnosis and vaccine development. In order to determine whether ZIKV exhibits strain-dependent activity when exposed to antibodies, we measured the neutralizing properties of polyclonal serum and three monoclonal antibodies (ZKA185, 753(3)C10, and 4G2) against three strains of ZIKV (MR−766, PRVABC59, and R103454). Here, MR−766 was inhibited almost 60% less by ZKA185 than PRVABC59 and R103454 (p = 0.008). ZKA185 enhanced dengue 4 infection up to 50% (p = 0.0058). PRVABC59 was not inhibited by mAb 753(3)C10 while MR−766 and R103453 were inhibited up to 90% (p = 0.04 and 0.036, respectively). Patient serum, regardless of exposure history, neutralized MR−766 ~30%−40% better than PRVABC56 or R103454 (p = 0.005−0.00007). The most troubling finding was the significant neutralization of MR−766 by patients with no ZIKV exposure. We also evaluated ZIKV antibody cross reactivity with various flaviviruses and found that more patients developed cross-reactive antibodies to Japanese encephalitis virus than the dengue viruses. The data here show that serological diagnosis of ZIKV is complicated and that qualitative neutralization assays cannot discriminate between flaviviruses.
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Affiliation(s)
- Kelli L. Barr
- Department of Biology, Baylor University, Waco, TX 76798, USA
- Correspondence:
| | - Erika R. Schwarz
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA; (E.R.S.); (D.P.); (R.P.); (M.T.L.)
| | - Dhani Prakoso
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA; (E.R.S.); (D.P.); (R.P.); (M.T.L.)
| | - Kehkashan Imtiaz
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi 74800, Pakistan; (K.I.); (E.K.)
| | - Ruiyu Pu
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA; (E.R.S.); (D.P.); (R.P.); (M.T.L.)
| | - J. Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32601, USA;
| | - Erum Khan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi 74800, Pakistan; (K.I.); (E.K.)
| | - Maureen T. Long
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA; (E.R.S.); (D.P.); (R.P.); (M.T.L.)
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Abdullah AA, Lee YK, Chin SP, Lim SK, Lee VS, Othman R, Othman S, Rahman NA, Yusof R, Heh CH. Discovery of Dengue Virus Inhibitors. Curr Med Chem 2020; 27:4945-5036. [PMID: 30514185 DOI: 10.2174/0929867326666181204155336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/11/2018] [Accepted: 11/22/2018] [Indexed: 11/22/2022]
Abstract
To date, there is still no approved anti-dengue agent to treat dengue infection in the market. Although the only licensed dengue vaccine, Dengvaxia is available, its protective efficacy against serotypes 1 and 2 of dengue virus was reported to be lower than serotypes 3 and 4. Moreover, according to WHO, the risk of being hospitalized and having severe dengue increased in seronegative individuals after they received Dengvaxia vaccination. Nevertheless, various studies had been carried out in search of dengue virus inhibitors. These studies focused on the structural (C, prM, E) and non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5) of dengue virus as well as host factors as drug targets. Hence, this article provides an overall up-to-date review of the discovery of dengue virus inhibitors that are only targeting the structural and non-structural viral proteins as drug targets.
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Affiliation(s)
- Adib Afandi Abdullah
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Yean Kee Lee
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Sek Peng Chin
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - See Khai Lim
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Vannajan Sanghiran Lee
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Rozana Othman
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Shatrah Othman
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Noorsaadah Abdul Rahman
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Rohana Yusof
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Choon Han Heh
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
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Yang CC, Hu HS, Lin HM, Wu PS, Wu RH, Tian JN, Wu SH, Tsou LK, Song JS, Chen HW, Chern JH, Chen CT, Yueh A. A novel flavivirus entry inhibitor, BP34610, discovered through high-throughput screening with dengue reporter viruses. Antiviral Res 2019; 172:104636. [PMID: 31654671 DOI: 10.1016/j.antiviral.2019.104636] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/24/2019] [Accepted: 10/20/2019] [Indexed: 12/01/2022]
Abstract
Dengue virus (DENV) is a global health problem that affects approximately 3.9 billion people worldwide. Since safety concerns were raised for the only licensed vaccine, Dengvaxia, and since the present treatment is only supportive care, the development of more effective therapeutic anti-DENV agents is urgently needed. In this report, we identified a potential small-molecule inhibitor, BP34610, via cell-based high-throughput screening (HTS) of 12,000 compounds using DENV-2 reporter viruses. BP34610 reduced the virus yields of type 2 DENV-infected cells with a 50% effective concentration (EC50) and selectivity index value of 0.48 ± 0.06 μM and 197, respectively. Without detectable cytotoxicity, the compound inhibited not only all four serotypes of DENV but also Japanese encephalitis virus (JEV). Time-of-addition experiments suggested that BP34610 may act at an early stage of DENV virus infection. Sequencing analyses of several individual clones derived from BP34610-resistant viruses revealed a consensus amino acid substitution (S397P) in the N-terminal stem region of the E protein. Introduction of S397P into the DENV reporter viruses conferred an over 14.8-fold EC90 shift for BP34610. Importantly, the combination of BP34610 with a viral replication inhibitor, ribavirin, displayed synergistic enhancement of anti-DENV-2 activity. Our results identify an effective small-molecule inhibitor, BP34610, which likely targets the DENV E protein. BP34610 could be developed as an anti-flavivirus agent in the future.
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Affiliation(s)
- Chi-Chen Yang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No.35, Keyan Road, Zhunan Town, Miaoli, 35053, Taiwan, ROC
| | - Han-Shu Hu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No.35, Keyan Road, Zhunan Town, Miaoli, 35053, Taiwan, ROC
| | - Hui-Mei Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No.35, Keyan Road, Zhunan Town, Miaoli, 35053, Taiwan, ROC
| | - Pei-Shan Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No.35, Keyan Road, Zhunan Town, Miaoli, 35053, Taiwan, ROC
| | - Ren-Huang Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No.35, Keyan Road, Zhunan Town, Miaoli, 35053, Taiwan, ROC
| | - Jia-Ni Tian
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No.35, Keyan Road, Zhunan Town, Miaoli, 35053, Taiwan, ROC; Department of Life Sciences, National Central University, Jhongli, Taiwan, ROC
| | - Szu-Huei Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No.35, Keyan Road, Zhunan Town, Miaoli, 35053, Taiwan, ROC
| | - Lun Kelvin Tsou
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No.35, Keyan Road, Zhunan Town, Miaoli, 35053, Taiwan, ROC
| | - Jen-Shin Song
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No.35, Keyan Road, Zhunan Town, Miaoli, 35053, Taiwan, ROC
| | - Hsin-Wei Chen
- Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, No.35, Keyan Road, Zhunan Town, Miaoli, 35053, Taiwan, ROC
| | - Jyh-Haur Chern
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No.35, Keyan Road, Zhunan Town, Miaoli, 35053, Taiwan, ROC
| | - Chiung-Tong Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No.35, Keyan Road, Zhunan Town, Miaoli, 35053, Taiwan, ROC
| | - Andrew Yueh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No.35, Keyan Road, Zhunan Town, Miaoli, 35053, Taiwan, ROC.
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32
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Schuler J, Samudrala R. Fingerprinting CANDO: Increased Accuracy with Structure- and Ligand-Based Shotgun Drug Repurposing. ACS OMEGA 2019; 4:17393-17403. [PMID: 31656912 PMCID: PMC6812124 DOI: 10.1021/acsomega.9b02160] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/30/2019] [Indexed: 05/08/2023]
Abstract
We have upgraded our Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun drug repurposing by including ligand-based, data fusion, and decision tree pipelines. The goal of shotgun drug repurposing is to screen and rank every existing human use drug or compound for every disease/indication. The first version of CANDO implemented a structure-based pipeline that modeled interactions between compounds and proteins on a large scale, generating compound-proteome interaction signatures used to infer the similarity of drug behavior; the new pipelines accomplish this by incorporating molecular fingerprints and the Tanimoto coefficient. We obtain improved benchmarking performance with the new pipelines across all three evaluation metrics used: average indication accuracy, pairwise accuracy, and coverage. The best performing pipeline achieves an average indication accuracy of 19.0% at the top10 cutoff, compared to 11.7% for v1, and 2.2% for a random control. Our results demonstrate that the CANDO drug recovery accuracy is substantially improved by integrating multiple pipelines, thereby enhancing our ability to generate putative therapeutic repurposing candidates, and increasing drug discovery efficiency.
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Affiliation(s)
- James Schuler
- Department of Biomedical
Informatics, Jacobs School of Medicine and
Biomedical Sciences at the University at Buffalo, Buffalo, New York 14203, United States
| | - Ram Samudrala
- Department of Biomedical
Informatics, Jacobs School of Medicine and
Biomedical Sciences at the University at Buffalo, Buffalo, New York 14203, United States
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33
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Fine J, Lackner R, Samudrala R, Chopra G. Computational chemoproteomics to understand the role of selected psychoactives in treating mental health indications. Sci Rep 2019; 9:13155. [PMID: 31511563 PMCID: PMC6739337 DOI: 10.1038/s41598-019-49515-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 07/31/2019] [Indexed: 12/17/2022] Open
Abstract
We have developed the Computational Analysis of Novel Drug Opportunities (CANDO) platform to infer homology of drug behaviour at a proteomic level by constructing and analysing structural compound-proteome interaction signatures of 3,733 compounds with 48,278 proteins in a shotgun manner. We applied the CANDO platform to predict putative therapeutic properties of 428 psychoactive compounds that belong to the phenylethylamine, tryptamine, and cannabinoid chemical classes for treating mental health indications. Our findings indicate that these 428 psychoactives are among the top-ranked predictions for a significant fraction of mental health indications, demonstrating a significant preference for treating such indications over non-mental health indications, relative to randomized controls. Also, we analysed the use of specific tryptamines for the treatment of sleeping disorders, bupropion for substance abuse disorders, and cannabinoids for epilepsy. Our innovative use of the CANDO platform may guide the identification and development of novel therapies for mental health indications and provide an understanding of their causal basis on a detailed mechanistic level. These predictions can be used to provide new leads for preclinical drug development for mental health and other neurological disorders.
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Affiliation(s)
- Jonathan Fine
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Rachel Lackner
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Ram Samudrala
- Department of Biomedical Informatics, SUNY, Buffalo, NY, USA.
| | - Gaurav Chopra
- Department of Chemistry, Purdue University, West Lafayette, IN, USA.
- Purdue Institute for Drug Discovery, Purdue Institute for Integrative Neuroscience, Purdue Institute for Integrative Neuroscience, Purdue Institute for Immunology, Inflammation and Infectious Disease, Integrative Data Science Initiative, Purdue Center for Cancer Research, West Lafayette, IN, USA.
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34
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Vilas Boas LCP, Campos ML, Berlanda RLA, de Carvalho Neves N, Franco OL. Antiviral peptides as promising therapeutic drugs. Cell Mol Life Sci 2019; 76:3525-3542. [PMID: 31101936 PMCID: PMC7079787 DOI: 10.1007/s00018-019-03138-w] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 05/04/2019] [Accepted: 05/07/2019] [Indexed: 01/28/2023]
Abstract
While scientific advances have led to large-scale production and widespread distribution of vaccines and antiviral drugs, viruses still remain a major cause of human diseases today. The ever-increasing reports of viral resistance and the emergence and re-emergence of viral epidemics pressure the health and scientific community to constantly find novel molecules with antiviral potential. This search involves numerous different approaches, and the use of antimicrobial peptides has presented itself as an interesting alternative. Even though the number of antimicrobial peptides with antiviral activity is still low, they already show immense potential to become pharmaceutically available antiviral drugs. Such peptides can originate from natural sources, such as those isolated from mammals and from animal venoms, or from artificial sources, when bioinformatics tools are used. This review aims to shed some light on antimicrobial peptides with antiviral activities against human viruses and update the data about the already well-known peptides that are still undergoing studies, emphasizing the most promising ones that may become medicines for clinical use.
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Affiliation(s)
| | - Marcelo Lattarulo Campos
- Centro de Análises Bioquímicas e Proteômicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, 70790-160, Brazil
- Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, 78060-900, Brazil
| | - Rhayfa Lorrayne Araujo Berlanda
- Centro de Análises Bioquímicas e Proteômicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, 70790-160, Brazil
| | - Natan de Carvalho Neves
- Centro de Análises Bioquímicas e Proteômicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, 70790-160, Brazil
| | - Octávio Luiz Franco
- Universidade de Brasília, Pós-Graduação em Patologia Molecular, Campus Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.
- Centro de Análises Bioquímicas e Proteômicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, 70790-160, Brazil.
- S-Inova Biotech, Pós-graduação em Biotecnologia Universidade Católica Dom Bosco, Campo Grande, MS, 79117-900, Brazil.
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35
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Chesnut M, Muñoz LS, Harris G, Freeman D, Gama L, Pardo CA, Pamies D. In vitro and in silico Models to Study Mosquito-Borne Flavivirus Neuropathogenesis, Prevention, and Treatment. Front Cell Infect Microbiol 2019; 9:223. [PMID: 31338335 PMCID: PMC6629778 DOI: 10.3389/fcimb.2019.00223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/11/2019] [Indexed: 01/07/2023] Open
Abstract
Mosquito-borne flaviviruses can cause disease in the nervous system, resulting in a significant burden of morbidity and mortality. Disease models are necessary to understand neuropathogenesis and identify potential therapeutics and vaccines. Non-human primates have been used extensively but present major challenges. Advances have also been made toward the development of humanized mouse models, but these models still do not fully represent human pathophysiology. Recent developments in stem cell technology and cell culture techniques have allowed the development of more physiologically relevant human cell-based models. In silico modeling has also allowed researchers to identify and predict transmission patterns and discover potential vaccine and therapeutic candidates. This review summarizes the research on in vitro and in silico models used to study three mosquito-borne flaviviruses that cause neurological disease in humans: West Nile, Dengue, and Zika. We also propose a roadmap for 21st century research on mosquito-borne flavivirus neuropathogenesis, prevention, and treatment.
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Affiliation(s)
- Megan Chesnut
- Center for Alternatives to Animal Testing, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Laura S. Muñoz
- Division of Neuroimmunology, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States,Neuroviruses Emerging in the Americas Study, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Georgina Harris
- Center for Alternatives to Animal Testing, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Dana Freeman
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Lucio Gama
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, United States,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Carlos A. Pardo
- Division of Neuroimmunology, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States,Neuroviruses Emerging in the Americas Study, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - David Pamies
- Center for Alternatives to Animal Testing, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States,Department of Physiology, University of Lausanne, Lausanne, Switzerland,*Correspondence: David Pamies
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36
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Lu Y, Qiu Q, Li C, Cheng L, Liu J. Computational identification of self-inhibitory peptides from white spot syndrome virus envelope protein VP28. AQUACULTURE REPORTS 2019; 14:100195. [PMID: 32289063 PMCID: PMC7104047 DOI: 10.1016/j.aqrep.2019.100195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/31/2019] [Accepted: 04/08/2019] [Indexed: 06/11/2023]
Abstract
Since effective chemotherapeutics or preventive measures are still unavailable, finding feasible approaches against white spot syndrome virus (WSSV) has always been the vital subject in shrimp farming field. Envelope proteins are the ideal targets for antiviral strategies development due to their indispensable roles in virus entry, and inhibitory peptides targeting them have been proved to be promising in blocking virus infection. In this study, the Wimley-White interfacial hydrophobicity scale (WWIHS) in combination with known structural data was applied to identify potential inhibitory peptides that targeted the envelope protein VP28 of WSSV. Results showed that two potential inhibitory peptides were identified, one of which exhibited not only obvious antiviral activity, but also broad-spectrum antimicrobial activity. The inhibitory peptide identified here can serve as a lead compound for anti-WSSV strategies development.
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Affiliation(s)
- Yongzhong Lu
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao University of Science and Technology, No. 53, Zhengzhou Road, 266042, Qingdao, China
| | - Qian Qiu
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao University of Science and Technology, No. 53, Zhengzhou Road, 266042, Qingdao, China
| | - Chen Li
- Yellow Sea Fisheries Research Institute, Chinese Academy Of Fishery Sciences, No. 106, Nanjing Road, 266071, Qingdao, China
| | - Linyue Cheng
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao University of Science and Technology, No. 53, Zhengzhou Road, 266042, Qingdao, China
| | - Jie Liu
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao University of Science and Technology, No. 53, Zhengzhou Road, 266042, Qingdao, China
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Huang YW, Lee CT, Wang TC, Kao YC, Yang CH, Lin YM, Huang KS. The Development of Peptide-based Antimicrobial Agents against Dengue Virus. Curr Protein Pept Sci 2019; 19:998-1010. [PMID: 29852867 PMCID: PMC6446661 DOI: 10.2174/1389203719666180531122724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/20/2018] [Accepted: 05/25/2018] [Indexed: 11/22/2022]
Abstract
Dengue fever has become an imminent threat to international public health because of global warming and climate change. The World Health Organization proclaimed that more than 50% of the world’s population is at risk of dengue virus (DENV) infection. Therefore, developing a clinically ap-proved vaccine and effective therapeutic remedy for treating dengue fever is imperative. Peptide drug de-velopment has become a novel pharmaceutical research field. This article reviews various peptides-based antimicrobial agents targeting three pathways involved in the DENV lifecycle. Specifically, they are peptide vaccines from immunomodulation, peptide drugs that inhibit virus entry, and peptide drugs that interfere with viral replication. Many antiviral peptide studies against DENV have been conducted in animal model trials, and progression to clinical trials for these promising peptide drugs is anticipated.
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Affiliation(s)
- Yen-Wei Huang
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan.,Department of Chinese Medicine, E-DA Hospital, Kaohsiung, Taiwan
| | - Chun-Ting Lee
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan.,Department of Chinese Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ta-Chen Wang
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan.,Department of Chinese Medicine, E-DA Hospital, Kaohsiung, Taiwan
| | - Yun-Chung Kao
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan.,Department of Chinese Medicine, Kuanshan Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taitung, Taiwan
| | - Chih-Hui Yang
- Department of Biological Science and Technology, I-Shou University, Kaohsiung, Taiwan
| | - Yu-Mei Lin
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan
| | - Keng-Shiang Huang
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan
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Isa DM, Chin SP, Chong WL, Zain SM, Rahman NA, Lee VS. Dynamics and binding interactions of peptide inhibitors of dengue virus entry. J Biol Phys 2019; 45:63-76. [PMID: 30680580 DOI: 10.1007/s10867-018-9515-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/28/2018] [Indexed: 01/01/2023] Open
Abstract
In this study, we investigate the binding interactions of two synthetic antiviral peptides (DET2 and DET4) on type II dengue virus (DENV2) envelope protein domain III. These two antiviral peptides are designed based on the domain III of the DENV2 envelope protein, which has shown significant inhibition activity in previous studies and can be potentially modified further to be active against all dengue strains. Molecular docking was performed using AutoDock Vina and the best-ranked peptide-domain III complex was further explored using molecular dynamics simulations. Molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) was used to calculate the relative binding free energies and to locate the key residues of peptide-protein interactions. The predicted binding affinity correlated well with the previous experimental studies. DET4 outperformed DET2 and is oriented within the binding site through favorable vdW and electrostatic interactions. Pairwise residue decomposition analysis has revealed several key residues that contribute to the binding of these peptides. Residues in DET2 interact relatively lesser with the domain III compared to DET4. Dynamic cross-correlation analysis showed that both the DET2 and DET4 trigger different dynamic patterns on the domain III. Correlated motions were seen between the residue pairs of DET4 and the binding site while binding of DET2 results in anti-correlated motion on the binding site. This work showcases the use of computational study in elucidating and explaining the experiment observation on an atomic level.
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Affiliation(s)
- Diyana Mohd Isa
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sek Peng Chin
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Wei Lim Chong
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sharifuddin M Zain
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Noorsaadah Abd Rahman
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Vannajan Sanghiran Lee
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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39
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Mangione W, Samudrala R. Identifying Protein Features Responsible for Improved Drug Repurposing Accuracies Using the CANDO Platform: Implications for Drug Design. Molecules 2019; 24:molecules24010167. [PMID: 30621144 PMCID: PMC6337359 DOI: 10.3390/molecules24010167] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/21/2018] [Accepted: 12/29/2018] [Indexed: 01/17/2023] Open
Abstract
Drug repurposing is a valuable tool for combating the slowing rates of novel therapeutic discovery. The Computational Analysis of Novel Drug Opportunities (CANDO) platform performs shotgun repurposing of 2030 indications/diseases using 3733 drugs/compounds to predict interactions with 46,784 proteins and relating them via proteomic interaction signatures. The accuracy is calculated by comparing interaction similarities of drugs approved for the same indications. We performed a unique subset analysis by breaking down the full protein library into smaller subsets and then recombining the best performing subsets into larger supersets. Up to 14% improvement in accuracy is seen upon benchmarking the supersets, representing a 100⁻1000-fold reduction in the number of proteins considered relative to the full library. Further analysis revealed that libraries comprised of proteins with more equitably diverse ligand interactions are important for describing compound behavior. Using one of these libraries to generate putative drug candidates against malaria, tuberculosis, and large cell carcinoma results in more drugs that could be validated in the biomedical literature compared to using those suggested by the full protein library. Our work elucidates the role of particular protein subsets and corresponding ligand interactions that play a role in drug repurposing, with implications for drug design and machine learning approaches to improve the CANDO platform.
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Affiliation(s)
- William Mangione
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14203, USA.
| | - Ram Samudrala
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14203, USA.
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40
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In vitro analysis of synthetic peptides in blocking the entry of dengue virus. Virus Res 2019; 260:142-150. [DOI: 10.1016/j.virusres.2018.11.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 11/29/2018] [Accepted: 11/29/2018] [Indexed: 12/20/2022]
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41
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Saikia S, Bordoloi M, Sarmah R, Kolita B. Antiviral compound screening, peptide designing, and protein network construction of influenza a virus (strain a/Puerto Rico/8/1934 H1N1). Drug Dev Res 2018; 80:106-124. [PMID: 30276835 DOI: 10.1002/ddr.21475] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 11/11/2022]
Abstract
Plant-based antiviral therapy is the current need for holistic health care management, which can be achieved through screening of phytochemicals and designing of antiviral peptides. There exist certain host's factors which are directly involved for rapid viral replication causing worldwide pandemic. A total of 177 phytochemicals from Ocimum sanctum (L.), Tinospora cordifolia (Thunb.) Miers, Cinnamomum camphora (L.) J. Presl., Allium sativum (L.), Curcuma longa (L.), and Aloe vera (L.) Burm. f. were evaluated for their affinity to all viral proteins of H1N1. Applying drug filters and keeping the threshold of such filters relative to the standards, 82 compounds were found suitable for further analysis. Consensus scoring system was used for screening top ligands from 82 compounds, which screened the top 12 compounds. Highly conserved regions (>80%) which were hydrophilic, flexible, antigenic, and also charged were screened out as potent antiviral peptides. The viral proteins were taken as the targets for the modeled peptides for protein-protein docking. Further, host-pathogen interacting network was constructed to unveil host factors involved in viral replication, from which unique protein clusters representing their involvement in viral reproduction were selected through mapping with pathway databases. Twelve compounds and five peptides were found to be highly effective against all the proteins of H1N1. Based on the uniqueness, 13 clusters of proteins were obtained which are engaged in cellular process, namely, viral reproduction, fructose-6-phosphate metabolism, nitrogen compound metabolism, biosynthesis, cellular process, oligodendrocyte development, localization, multiorganism process, primary metabolism, response to unfolded protein, metabolism, and response to protein and catabolism.
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Affiliation(s)
- Surovi Saikia
- Chemical Sciences & Technology (Natural Products Chemistry) Division, CSIR North East Institute of Science & Technology, Jorhat, Assam, India
| | - Manobjyoti Bordoloi
- Chemical Sciences & Technology (Natural Products Chemistry) Division, CSIR North East Institute of Science & Technology, Jorhat, Assam, India
| | - Rajeev Sarmah
- Allied Health Sciences, Assam Down Town University, Panikhaiti, Guwahati, Assam, India
| | - Bhaskor Kolita
- Chemical Sciences & Technology (Natural Products Chemistry) Division, CSIR North East Institute of Science & Technology, Jorhat, Assam, India
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42
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Gomes B, Augusto MT, Felício MR, Hollmann A, Franco OL, Gonçalves S, Santos NC. Designing improved active peptides for therapeutic approaches against infectious diseases. Biotechnol Adv 2018; 36:415-429. [PMID: 29330093 DOI: 10.1016/j.biotechadv.2018.01.004] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 12/13/2017] [Accepted: 01/06/2018] [Indexed: 12/25/2022]
Abstract
Infectious diseases are one of the main causes of human morbidity and mortality. In the last few decades, pathogenic microorganisms' resistance to conventional drugs has been increasing, and it is now pinpointed as a major worldwide health concern. The need to search for new therapeutic options, as well as improved treatment outcomes, has therefore increased significantly, with biologically active peptides representing a new alternative. A substantial research effort is being dedicated towards their development, especially due to improved biocompatibility and target selectivity. However, the inherent limitations of peptide drugs are restricting their application. In this review, we summarize the current status of peptide drug development, focusing on antiviral and antimicrobial peptide activities, highlighting the design improvements needed, and those already being used, to overcome the drawbacks of the therapeutic application of biologically active peptides.
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Affiliation(s)
- Bárbara Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Marcelo T Augusto
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Mário R Felício
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Axel Hollmann
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal; Laboratory of Molecular Microbiology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Buenos Aires, Argentina; Laboratory of Biointerfaces and Biomimetic Systems, CITSE, National University of Santiago del Estero-CONICET, Santiago del Estero, Argentina
| | - Octávio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, DF, Brazil; S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Sónia Gonçalves
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal.
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Chopra G, Samudrala R. Exploring Polypharmacology in Drug Discovery and Repurposing Using the CANDO Platform. Curr Pharm Des 2017; 22:3109-23. [PMID: 27013226 DOI: 10.2174/1381612822666160325121943] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 03/01/2015] [Indexed: 01/05/2023]
Abstract
BACKGROUND Traditional drug discovery approaches focus on a limited set of target molecules for treatment against specific indications/diseases. However, drug absorption, dispersion, metabolism, and excretion (ADME) involve interactions with multiple protein systems. Drugs approved for particular indication(s) may be repurposed as novel therapeutics for others. The severely declining rate of discovery and increasing costs of new drugs illustrate the limitations of the traditional reductionist paradigm in drug discovery. METHODS We developed the Computational Analysis of Novel Drug Opportunities (CANDO) platform based on a hypothesis that drugs function by interacting with multiple protein targets to create a molecular interaction signature that can be exploited for therapeutic repurposing and discovery. We compiled a library of compounds that are human ingestible with minimal side effects, followed by an 'all-compounds' vs 'all-proteins' fragment-based multitarget docking with dynamics screen to construct compound-proteome interaction matrices that were then analyzed to determine similarity of drug behavior. The proteomic signature similarity of drugs is then ranked to make putative drug predictions for all indications in a shotgun manner. RESULTS We have previously applied this platform with success in both retrospective benchmarking and prospective validation, and to understand the effect of druggable protein classes on repurposing accuracy. Here we use the CANDO platform to analyze and determine the contribution of multitargeting (polypharmacology) to drug repurposing benchmarking accuracy. Taken together with the previous work, our results indicate that a large number of protein structures with diverse fold space and a specific polypharmacological interactome is necessary for accurate drug predictions using our proteomic and evolutionary drug discovery and repurposing platform. CONCLUSION These results have implications for future drug development and repurposing in the context of polypharmacology.
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Affiliation(s)
- Gaurav Chopra
- Department of Chemistry, Purdue University, West Lafayette, IN, USA.
| | - Ram Samudrala
- Department of Biomedical Informatics, SUNY, Buffalo, NY, USA.
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44
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Petersen RL. Strategies Using Bio-Layer Interferometry Biosensor Technology for Vaccine Research and Development. BIOSENSORS-BASEL 2017; 7:bios7040049. [PMID: 29088096 PMCID: PMC5746772 DOI: 10.3390/bios7040049] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/26/2017] [Accepted: 10/28/2017] [Indexed: 12/13/2022]
Abstract
Bio-layer interferometry (BLI) real-time, label-free technology has greatly contributed to advances in vaccine research and development. BLI Octet platforms offer high-throughput, ease of use, reliability, and high precision analysis when compared with common labeling techniques. Many different strategies have been used to immobilize the pathogen or host molecules on BLI biosensors for real-time kinetics and affinity analysis, quantification, or high-throughput titer. These strategies can be used in multiple applications and shed light onto the structural and functional aspects molecules play during pathogen-host interactions. They also provide crucial information on how to achieve protection. This review summarizes some key BLI strategies used in human vaccine research and development.
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45
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Atkins C, Freiberg AN. Recent advances in the development of antiviral therapeutics for Rift Valley fever virus infection. Future Virol 2017; 12:651-665. [PMID: 29181086 DOI: 10.2217/fvl-2017-0060] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/26/2017] [Indexed: 12/25/2022]
Abstract
Rift Valley fever virus (RVFV) is a mosquito-borne bunyavirus endemic to sub-Saharan Africa and the Arabian Peninsula and the etiological agent of Rift Valley fever. Rift Valley fever is a disease of major public health and economic concern, affecting livestock and humans. In ruminants, RVFV infection is characterized by high mortality rates in newborns and near 100% abortion rates in pregnant animals. Infection in humans is typically manifested as a self-limiting febrile illness, but can lead to severe and fatal hepatitis, encephalitis, hemorrhagic fever or retinitis with partial or complete blindness. Currently, there are no specific treatment options available for RVFV infection. This review presents a summary of the therapeutic approaches that have been explored on the treatment of RVFV infection.
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Affiliation(s)
- Colm Atkins
- Department of Pathology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,Department of Pathology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Alexander N Freiberg
- Department of Pathology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,The Sealy Center for Vaccine Development, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,The Center for Biodefense & Emerging Infectious Diseases, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,Department of Pathology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,The Sealy Center for Vaccine Development, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,The Center for Biodefense & Emerging Infectious Diseases, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
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46
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Chew MF, Poh KS, Poh CL. Peptides as Therapeutic Agents for Dengue Virus. Int J Med Sci 2017; 14:1342-1359. [PMID: 29200948 PMCID: PMC5707751 DOI: 10.7150/ijms.21875] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/01/2017] [Indexed: 12/19/2022] Open
Abstract
Dengue is an important global threat caused by dengue virus (DENV) that records an estimated 390 million infections annually. Despite the availability of CYD-TDV as a commercial vaccine, its long-term efficacy against all four dengue virus serotypes remains unsatisfactory. There is therefore an urgent need for the development of antiviral drugs for the treatment of dengue. Peptide was once a neglected choice of medical treatment but it has lately regained interest from the pharmaceutical industry following pioneering advancements in technology. In this review, the design of peptide drugs, antiviral activities and mechanisms of peptides and peptidomimetics (modified peptides) action against dengue virus are discussed. The development of peptides as inhibitors for viral entry, replication and translation is also described, with a focus on the three main targets, namely, the host cell receptors, viral structural proteins and viral non-structural proteins. The antiviral peptides designed based on these approaches may lead to the discovery of novel anti-DENV therapeutics that can treat dengue patients.
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Affiliation(s)
- Miaw-Fang Chew
- Research Centre for Biomedical Sciences, Sunway University, Bandar Sunway, Selangor 47500, Malaysia
| | - Keat-Seong Poh
- Department of Surgery, Faculty of Medicine, University of Malaya, Jalan Universiti, Kuala Lumpur, 50603, Malaysia
| | - Chit-Laa Poh
- Research Centre for Biomedical Sciences, Sunway University, Bandar Sunway, Selangor 47500, Malaysia
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47
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Combating Ebola with Repurposed Therapeutics Using the CANDO Platform. Molecules 2016; 21:molecules21121537. [PMID: 27898018 PMCID: PMC5958544 DOI: 10.3390/molecules21121537] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/23/2016] [Accepted: 10/28/2016] [Indexed: 12/20/2022] Open
Abstract
Ebola virus disease (EVD) is extremely virulent with an estimated mortality rate of up to 90%. However, the state-of-the-art treatment for EVD is limited to quarantine and supportive care. The 2014 Ebola epidemic in West Africa, the largest in history, is believed to have caused more than 11,000 fatalities. The countries worst affected are also among the poorest in the world. Given the complexities, time, and resources required for a novel drug development, finding efficient drug discovery pathways is going to be crucial in the fight against future outbreaks. We have developed a Computational Analysis of Novel Drug Opportunities (CANDO) platform based on the hypothesis that drugs function by interacting with multiple protein targets to create a molecular interaction signature that can be exploited for rapid therapeutic repurposing and discovery. We used the CANDO platform to identify and rank FDA-approved drug candidates that bind and inhibit all proteins encoded by the genomes of five different Ebola virus strains. Top ranking drug candidates for EVD treatment generated by CANDO were compared to in vitro screening studies against Ebola virus-like particles (VLPs) by Kouznetsova et al. and genetically engineered Ebola virus and cell viability studies by Johansen et al. to identify drug overlaps between the in virtuale and in vitro studies as putative treatments for future EVD outbreaks. Our results indicate that integrating computational docking predictions on a proteomic scale with results from in vitro screening studies may be used to select and prioritize compounds for further in vivo and clinical testing. This approach will significantly reduce the lead time, risk, cost, and resources required to determine efficacious therapies against future EVD outbreaks.
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Abstract
INTRODUCTION Flaviviruses are major causes of infectious disease. The vast global, social and economic impact due to morbidity and mortality associated with diseases caused by these viruses urgently demands effective therapeutic interventions. There is currently no specific antiviral therapy available for the effective clinical treatment of infections by any of the flaviviridae. Development of more effective vaccines and antiviral agents for the prevention and treatment of most flavivirus infections remains a clear public health priority in the 21st century. AREAS COVERED This review describes some of the recent discoveries in the field of flavivirus inhibitor development, with a particular focus on targeting viral proteins. Emphasis is placed on the advances published during the 2012-2015 period. EXPERT OPINION The field of drug discovery targeting viral proteins has progressed slowly in recent years. New information, particularly on structures, location and mechanisms of action of established protein targets have been reported. There have also been studies on repurposing known drugs as templates for targeting flavivirus proteins and these hits could be promising templates for developing new more potent inhibitors. Further research should be conducted to improve in vitro assays that better reflect the conditions found in cellular environments.
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Affiliation(s)
- W Mei Kok
- a Division of Chemistry and Structural Biology, Institute for Molecular Bioscience , The University of Queensland , Brisbane , Australia
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49
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Abstract
The dengue virus and related flaviviruses are an increasing global health threat. In this perspective, we comment on and review medicinal chemistry efforts aimed at the prevention or treatment of dengue infections. We include target-based approaches aimed at viral or host factors and results from phenotypic screenings in cellular assay systems for viral replication. This perspective is limited to the discussion of results that provide explicit chemistry or structure-activity relationship (SAR), or appear to be of particular interest to the medicinal chemist for other reasons. The discovery and development efforts discussed here may at least partially be extrapolated toward other emerging flaviviral infections, such as West Nile virus. Therefore, this perspective, although not aimed at flaviviruses in general, should also be able to provide an overview of the medicinal chemistry of these closely related infectious agents.
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Affiliation(s)
- Mira A M Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Christoph Nitsche
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Veaceslav Boldescu
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany.,Laboratory of Organic Synthesis, Institute of Chemistry of the Academy of Sciences of Moldova , Academiei 3, 2028 Chisinau, Moldova
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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50
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Manvar D, Küçükgüzel İ, Erensoy G, Tatar E, Deryabaşoğulları G, Reddy H, Talele TT, Cevik O, Kaushik-Basu N. Discovery of conjugated thiazolidinone-thiadiazole scaffold as anti-dengue virus polymerase inhibitors. Biochem Biophys Res Commun 2016; 469:743-7. [DOI: 10.1016/j.bbrc.2015.12.042] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 12/11/2015] [Indexed: 11/29/2022]
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