1
|
Rehman HM, Sajjad M, Ali MA, Gul R, Irfan M, Naveed M, Bhinder MA, Ghani MU, Hussain N, Said ASA, Al Haddad AHI, Saleem M. Identification of NS2B-NS3 Protease Inhibitors for Therapeutic Application in ZIKV Infection: A Pharmacophore-Based High-Throughput Virtual Screening and MD Simulations Approaches. Vaccines (Basel) 2023; 11:vaccines11010131. [PMID: 36679976 PMCID: PMC9862652 DOI: 10.3390/vaccines11010131] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Zika virus (ZIKV) pandemic and its implication in congenital malformations and severe neurological disorders had created serious threats to global health. ZIKV is a mosquito-borne flavivirus which spread rapidly and infect a large number of people in a shorter time-span. Due to the lack of effective therapeutics, this had become paramount urgency to discover effective drug molecules to encounter the viral infection. Various anti-ZIKV drug discovery efforts during the past several years had been unsuccessful to develop an effective cure. The NS2B-NS3 protein was reported as an attractive therapeutic target for inhibiting viral proliferation, due to its central role in viral replication and maturation of non-structural viral proteins. Therefore, the current in silico drug exploration aimed to identify the novel inhibitors of Zika NS2B-NS3 protease by implementing an e-pharmacophore-based high-throughput virtual screening. A 3D e-pharmacophore model was generated based on the five-featured (ADPRR) pharmacophore hypothesis. Subsequently, the predicted model is further subjected to the high-throughput virtual screening to reveal top hit molecules from the various small molecule databases. Initial hits were examined in terms of binding free energies and ADME properties to identify the candidate hit exhibiting a favourable pharmacokinetic profile. Eventually, molecular dynamic (MD) simulations studies were conducted to evaluate the binding stability of the hit molecule inside the receptor cavity. The findings of the in silico analysis manifested affirmative evidence for three hit molecules with -64.28, -55.15 and -50.16 kcal/mol binding free energies, as potent inhibitors of Zika NS2B-NS3 protease. Hence, these molecules holds the promising potential to serve as a prospective candidates to design effective drugs against ZIKV and related viral infections.
Collapse
Affiliation(s)
- Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Quaid e Azam Campus, Lahore 54590, Punjab, Pakistan
| | - Muhammad Akhtar Ali
- School of Biological Sciences, University of the Punjab, Quaid e Azam Campus, Lahore 54590, Punjab, Pakistan
| | - Roquyya Gul
- Faculty of Life Sciences, Gulab Devi Educational Complex, Lahore 54590, Punjab, Pakistan
| | - Muhammad Irfan
- Kauser Abdulla Malik School of Life Sciences, Forman Christian College (A Chartered University), Lahore 54600, Punjab, Pakistan
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab Lahore, Lahore 54590, Punjab, Pakistan
| | - Munir Ahmad Bhinder
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan
| | - Muhammad Usman Ghani
- Center for Applied Molecular Biology, University of the Punjab, Lahore 54590, Punjab, Pakistan
| | - Nadia Hussain
- Department of Pharmaceutical Sciences, College of Pharmacy, Al Ain University, Al Ain 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 112612, United Arab Emirates
| | - Amira S. A. Said
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 112612, United Arab Emirates
- Department of Clinical Pharmacy, College of Pharmacy, Al Ain University, Al Ain 64141, United Arab Emirates
- Clinical Pharmacy Department, Faculty of Pharmacy, Beni Suef University, Beni Suef 62521, Egypt
| | - Amal H. I. Al Haddad
- Chief Operations Office, Sheikh Shakhbout Medical City (SSMC) in Partnership with Mayo Clinic, Abu Dhabi 11001, United Arab Emirates
| | - Mahjabeen Saleem
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan
- School of Medical Lab Technology, Minhaj University Lahore, Lahore 54770, Punjab, Pakistan
- Correspondence:
| |
Collapse
|
2
|
In silico identification of novel allosteric inhibitors of dengue virus NS2B/NS3 serine protease. JOURNAL OF THE SERBIAN CHEMICAL SOCIETY 2022. [DOI: 10.2298/jsc210929011d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Although dengue is a disease that affects more than 100 countries and puts
almost 400 million lives at risk each year, there is no approved antiviral
in the treatment of this pathology. In this context, proteases are potential
biological targets since they are essential in the replication process of
this virus. In this study, a library of more than 3,000 structures was used
to explore the allosteric inhibition of the NS2B/NS3 protease complex
using Consensual Docking techniques. The results show four best ranked
structures that were selected for molecular dynamics and free energy
simulations. Our analysis corroborate with other studies (experimental and
theoretical) presented in the literature. Thus, the computational approach
used here proved to be useful for planning new inhibitors in the combat
against Dengue disease.
Collapse
|
3
|
Alves KMA, Cardoso FJB, Honorio KM, de Molfetta FA. Design of Inhibitors for Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) Enzyme of <i>Leishmania mexicana</i>. Med Chem 2021; 16:784-795. [PMID: 31309897 DOI: 10.2174/1573406415666190712111139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/24/2019] [Accepted: 06/24/2019] [Indexed: 01/04/2023]
Abstract
BACKGROUND Leishmaniosis is a neglected tropical disease and glyceraldehyde 3- phosphate dehydrogenase (GAPDH) is a key enzyme in the design of new drugs to fight this disease. OBJECTIVE The present study aimed to evaluate potential inhibitors of GAPDH enzyme found in Leishmania mexicana (L. mexicana). METHODS A search for novel antileishmanial molecules was carried out based on similarities from the pharmacophoric point of view related to the binding site of the crystallographic enzyme using the ZINCPharmer server. The molecules selected in this screening were subjected to molecular docking and molecular dynamics simulations. RESULTS Consensual analysis of the docking energy values was performed, resulting in the selection of ten compounds. These ligand-receptor complexes were visually inspected in order to analyze the main interactions and subjected to toxicophoric evaluation, culminating in the selection of three compounds, which were subsequently submitted to molecular dynamics simulations. The docking results showed that the selected compounds interacted with GAPDH from L. mexicana, especially by hydrogen bonds with Cys166, Arg249, His194, Thr167, and Thr226. From the results obtained from molecular dynamics, it was observed that one of the loop regions, corresponding to the residues 195-222, can be related to the fitting of the substrate at the binding site, assisting in the positioning and the molecular recognition via residues responsible for the catalytic activity. CONCLUSION The use of molecular modeling techniques enabled the identification of promising compounds as inhibitors of the GAPDH enzyme from L. mexicana, and the results obtained here can serve as a starting point to design new and more effective compounds than those currently available.
Collapse
Affiliation(s)
- Krisnna M A Alves
- Laboratorio de Modelagem Molecular, Instituto de Ciencias Exatas e Naturais, Universidade Federal do Para, CP 11101, 60075-110, Belem, PA, Brazil
| | - Fábio José Bonfim Cardoso
- Laboratorio de Modelagem Molecular, Instituto de Ciencias Exatas e Naturais, Universidade Federal do Para, CP 11101, 60075-110, Belem, PA, Brazil
| | - Kathia M Honorio
- Escola de Artes, Ciencias e Humanidades, Universidade de Sao Paulo (USP), 03828-000, Sao Paulo, SP, Brazil.,Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Fábio A de Molfetta
- Laboratorio de Modelagem Molecular, Instituto de Ciencias Exatas e Naturais, Universidade Federal do Para, CP 11101, 60075-110, Belem, PA, Brazil
| |
Collapse
|
4
|
Cardoso FJB, Xavier LP, Santos AV, Pereira HD, Santos LDS, Molfetta FAD. Identification of potential inhibitors of Schistosoma mansoni purine nucleoside phosphorylase from neolignan compounds using molecular modelling approaches. J Biomol Struct Dyn 2021; 40:8248-8260. [PMID: 33830889 DOI: 10.1080/07391102.2021.1910073] [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: 10/21/2022]
Abstract
Schistosomiasis is a parasitic disease that is part of the neglected tropical diseases (NTDs), which cause significant levels of morbidity and mortality in millions of people throughout the world. The enzyme purine nucleoside phosphorylase from Schistosoma mansoni (SmPNP) represents a potential target for discovering new agents, and neolignans stand out as an important class of compounds. In this work, molecular modeling studies and biological assays of a set of neolignans were conducted against the PNP enzymes of the parasite and the human homologue (HssPNP). The results of the molecular docking described that the neolignans showed good complementarity by the active site of SmPNP. Molecular dynamics (MD) studies revealed that both complexes (Sm/HssPNP - neolignan compounds) were stable by analyzing the root mean square deviation (RMSD) values, and the binding free energy values suggest that the selected structures can interact and inhibit the catalytic activity of the SmPNP. Finally, the biological assay indicated that the selected neolignans presented a better molecular profile of inhibition compared to the human enzyme, as these ligands did not have the capacity to inhibit enzymatic activity, indicating that these compounds are promising candidates and that they can be used in future research in chemotherapy for schistosomiasis.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Fábio José Bonfim Cardoso
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Luciana Pereira Xavier
- Laboratório de Biotecnologia de Enzimas e Biotransformação, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém-PA, Brazil
| | - Agenor Valadares Santos
- Laboratório de Biotecnologia de Enzimas e Biotransformação, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém-PA, Brazil
| | - Humberto D'Muniz Pereira
- Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos-SP, Brazil
| | - Lourivaldo da Silva Santos
- Laboratório de Síntese e Produtos Naturais, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém-PA, Brazil
| | - Fábio Alberto de Molfetta
- Laboratório de Modelagem Molecular, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
| |
Collapse
|
5
|
Rohini K, Agarwal P, Preethi B, Shanthi V, Ramanathan K. Exploring the Lead Compounds for Zika Virus NS2B-NS3 Protein: an e-Pharmacophore-Based Approach. Appl Biochem Biotechnol 2018; 187:194-210. [PMID: 29911269 DOI: 10.1007/s12010-018-2814-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/05/2018] [Indexed: 12/19/2022]
Abstract
The rapid spread of the Zika virus and its association with the abnormal brain development constitute a global health emergency. With a continuing spread of the mosquito vector, the exposure is expected to accelerate in the coming years. Despite number of efforts, there is still no proper vaccine or medicine to combat this virus. Of note, the NS2B-NS3 protein is proven to be the potential target for the Zika virus therapeutics. Hence, e-pharmacophore-based drug design strategy was employed to identify potent inhibitors of NS2B-NS3 protein from ASINEX database consisting of 467,802 molecules. A 3D e-pharmacophore model was generated using PHASE module of Schrödinger Suite. The generated model consists of one hydrogen bond acceptor (A), two hydrogen bond donors (D), and two aromatic rings (R), ADDRR. The model was further evaluated for its ability to screen actives using enrichment analysis. Subsequently, high-throughput virtual screening protocol was employed, and the resultant hit molecules were also examined for its binding free energies and ADME properties using Prime MM-GBSA and Qikprop module of Schrodinger packages, respectively. Finally, the screened hit molecule was subjected to molecular dynamics simulation to examine its stability. Overall, the results from our analysis suggest that compound BAS 19192837 could be a potent inhibitor for the NS2B-NS3 protein of the Zika virus. It is also noteworthy to mention that our results are in good agreement with literature evidences. We hope that this result is of immense importance in designing potential drug molecules to combat the spread of Zika virus in the near future.
Collapse
Affiliation(s)
- K Rohini
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, 632014, India
| | - Pratika Agarwal
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, 632014, India
| | - B Preethi
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, 632014, India
| | - V Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, 632014, India
| | - K Ramanathan
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, 632014, India.
| |
Collapse
|
6
|
Ligand-Based Pharmacophore Screening Strategy: a Pragmatic Approach for Targeting HER Proteins. Appl Biochem Biotechnol 2018; 186:85-108. [PMID: 29508211 DOI: 10.1007/s12010-018-2724-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/19/2018] [Indexed: 02/07/2023]
Abstract
Targeting ErbB family of receptors is an important therapeutic option, because of its essential role in the broad spectrum of human cancers, including non-small cell lung cancer (NSCLC). Therefore, in the present work, considerable effort has been made to develop an inhibitor against HER family proteins, by combining the use of pharmacophore modelling, docking scoring functions, and ADME property analysis. Initially, a five-point pharmacophore model was developed using known HER family inhibitors. The generated model was then used as a query to screen a total of 468,880 compounds of three databases namely ZINC, ASINEX, and DrugBank. Subsequently, docking analysis was carried out to obtain hit molecules that could inhibit the HER receptors. Further, analysis of GLIDE scores and ADME properties resulted in one hit namely BAS01025917 with higher glide scores, increased CNS involvement, and good pharmaceutically relevant properties than reference ligand, afatinib. Furthermore, the inhibitory activity of the lead compounds was validated by performing molecular dynamic simulations. Of note, BAS01025917 was found to possess scaffolds with a broad spectrum of antitumor activity. We believe that this novel hit molecule can be further exploited for the development of a pan-HER inhibitor with low toxicity and greater potential.
Collapse
|
7
|
Ragab HM, El Maksoud NA, Amin MA, Halim MH, Abdulla NA, Kamel A, Moussa SM. IL-21 as a Predictor of Sustained Virologic Response in Patients with Chronic Hepatitis C Virus Infection. Appl Biochem Biotechnol 2017; 185:484-493. [PMID: 29192391 DOI: 10.1007/s12010-017-2669-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 11/24/2017] [Indexed: 02/08/2023]
Abstract
Hepatitis C virus (HCV) infection is a significant public health problem. The crucial role of interleukin (IL)-21 in HCV has been established. Thus, we aimed to investigate the association of serum IL-21 levels with the virological response to interferon (IFN)-based therapy in a group of Egyptian patients with chronic hepatitis C (CHC). Clinical data were collected from 58 HCV-positive Egyptian patients treated with IFN/ribavirin therapy and 10 non-HCV-infected healthy subjects. Liver and renal function tests, complete blood count, viral markers, and pretreatment IL-21 levels were determined in all patients and healthy controls. Patients who achieved sustained virologic response (SVR) had higher pretreatment median serum IL-21 levels than those who did not. Thus, this study concluded that higher pretreatment serum IL-21 may be useful in predicting SVR in CHC patients.
Collapse
Affiliation(s)
- Halla Mohamed Ragab
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, Dokki, Giza, Egypt.
| | - Nabila Abd El Maksoud
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, Dokki, Giza, Egypt
| | - Mona A Amin
- Internal Medicine, Cairo University, Giza, Egypt
| | - Mohab H Halim
- Biochemistry Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, Dokki, Giza, Egypt
| | - Nour A Abdulla
- Hepatology Department, National Hepatology & Tropical Medicine Research Institute, Cairo, Egypt
| | - Abdelkarim Kamel
- Medical Biochemistry, Faculty of Medicine, Cairo University, Giza, Egypt
| | | |
Collapse
|
8
|
Drug Design for ALK-Positive NSCLC: an Integrated Pharmacophore-Based 3D QSAR and Virtual Screening Strategy. Appl Biochem Biotechnol 2017; 185:289-315. [DOI: 10.1007/s12010-017-2650-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/26/2017] [Indexed: 12/27/2022]
|
9
|
Ganesan A, Barakat K. Applications of computer-aided approaches in the development of hepatitis C antiviral agents. Expert Opin Drug Discov 2017; 12:407-425. [PMID: 28164720 DOI: 10.1080/17460441.2017.1291628] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Hepatitis C virus (HCV) is a global health problem that causes several chronic life-threatening liver diseases. The numbers of people affected by HCV are rising annually. Since 2011, the FDA has approved several anti-HCV drugs; while many other promising HCV drugs are currently in late clinical trials. Areas covered: This review discusses the applications of different computational approaches in HCV drug design. Expert opinion: Molecular docking and virtual screening approaches have emerged as a low-cost tool to screen large databases and identify potential small-molecule hits against HCV targets. Ligand-based approaches are useful for filtering-out compounds with rich physicochemical properties to inhibit HCV targets. Molecular dynamics (MD) remains a useful tool in optimizing the ligand-protein complexes and understand the ligand binding modes and drug resistance mechanisms in HCV. Despite their varied roles, the application of in-silico approaches in HCV drug design is still in its infancy. A more mature application should aim at modelling the whole HCV replicon in its active form and help to identify new effective druggable sites within the replicon system. With more technological advancements, the roles of computer-aided methods are only going to increase several folds in the development of next-generation HCV drugs.
Collapse
Affiliation(s)
- Aravindhan Ganesan
- a Faculty of Pharmacy and Pharmaceutical Sciences , University of Alberta , Edmonton , Canada
| | - Khaled Barakat
- a Faculty of Pharmacy and Pharmaceutical Sciences , University of Alberta , Edmonton , Canada
| |
Collapse
|
10
|
Abstract
It is now plausible to dock libraries of 10 million molecules against targets over several days or weeks. When the molecules screened are commercially available, they may be rapidly tested to find new leads. Although docking retains important liabilities (it cannot calculate affinities accurately nor even reliably rank order high-scoring molecules), it can often can distinguish likely from unlikely ligands, often with hit rates above 10%. Here we summarize the improvements in libraries, target quality, and methods that have supported these advances, and the open access resources that make docking accessible. Recent docking screens for new ligands are sketched, as are the binding, crystallographic, and in vivo assays that support them. Like any technique, controls are crucial, and key experimental ones are reviewed. With such controls, docking campaigns can find ligands with new chemotypes, often revealing the new biology that may be docking's greatest impact over the next few years.
Collapse
Affiliation(s)
- John J Irwin
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
| |
Collapse
|
11
|
Ramesh M, Vepuri SB, Oosthuizen F, Soliman ME. Adenosine Monophosphate-Activated Protein Kinase (AMPK) as a Diverse Therapeutic Target: A Computational Perspective. Appl Biochem Biotechnol 2015; 178:810-30. [DOI: 10.1007/s12010-015-1911-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 10/26/2015] [Indexed: 12/12/2022]
|