1
|
Negi S, Kamboj NK, K GB, Yadava U. Investigation of ritonavir analogs antiretroviral natural compounds against SARS-CoV-2 envelope protein. J Biomol Struct Dyn 2025; 43:874-889. [PMID: 39737750 DOI: 10.1080/07391102.2023.2283872] [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: 02/19/2023] [Accepted: 11/09/2023] [Indexed: 01/01/2025]
Abstract
Since the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported from Wuhan, China, there has been a surge in scientific research to find a permanent cure for the disease. The main challenge in effective drug discovery is the continuously mutating nature of the SARS-CoV-2 virus. Thus, we have used the I-TASSER modeling to predict the structure of the SARS-CoV-2 viral envelope protein followed by combinatorial computational assessment to predict its putative potential small molecule inhibitors. As early treatment with ritonavir in combination was associated with faster time to clinical improvement and/or virological clearance, we aimed to retrieve analogs of ritonavir to find ideal inhibitors for SARS-CoV-2 viral envelope protein. The collected ligands were screened against the predicted binding pocket of viral envelope protein using extra precision (XP) docking protocol and the first four best-docked compounds were studied for complex stability using 300 ns all-atom molecular dynamics simulations embedding within the cellular membrane. Among the selected compounds, ZINC64859171 and ZINC1221429 showed considerable stability and interactions by comparison to the reference compound, i.e., Ritonavir (ZINC3944422). Moreover, the post-simulation analysis suggested the considerable binding affinity and induced conformation changes in the respective docked complexes against Ritonavir. Altogether, the obtained results demonstrated the putative potential of screened ritonavir analogs, i.e., ZINC64859171, against the envelope protein of SARS-CoV-2 and can be considered for further drug development in the treatment of the COVID-19 pandemic.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shivani Negi
- Department of Physics, DDU Gorakhpur University, Gorakhpur, Uttar Pradesh, India
| | - Nitin Kumar Kamboj
- Department of Mathematics, School of Physical Sciences, DIT University, Dehradun, Uttarakhand, India
| | - Gireesh Babu K
- Department of Life Sciences, Parul Institute of Applied Sciences, Parul University, Limda, Gujarat, India
| | - Umesh Yadava
- Department of Physics, DDU Gorakhpur University, Gorakhpur, Uttar Pradesh, India
| |
Collapse
|
2
|
Paróczai D, Bikov A, Blidaru A, Bobu E, Lascu A, Mot CI, Mihaicuta S, Frent S. Comparative efficacy of repurposed drugs lopinavir-ritonavir and darunavir-ritonavir in hospitalised COVID-19 patients: insights from a tertiary centre cohort. Front Cell Infect Microbiol 2025; 14:1496176. [PMID: 39885967 PMCID: PMC11779713 DOI: 10.3389/fcimb.2024.1496176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Accepted: 12/26/2024] [Indexed: 02/01/2025] Open
Abstract
Background Drug repurposing has become a widely adopted strategy to minimise research time, costs, and associated risks. Combinations of protease inhibitors such as lopinavir and darunavir with ritonavir have been repurposed as treatments for COVID-19. Although lopinavir-ritonavir (LPV/r) and darunavir-ritonavir (DRV/r) have shown in vitro efficacy against COVID-19, the results in human studies have been inconsistent. Therefore, our objective was to compare the efficacy of LPV/r and DRV/r in COVID-19 patients admitted to a tertiary centre in Romania. Research design and methods A clinical dataset from 417 hospitalised patients was analysed. Patients were assigned to the LPV/r, DRV/r, or control (standard-of-care) group based on clinical decisions made by the attending infectious disease specialists, aligned with national treatment protocols. Kaplan-Meier and Cox proportional hazards regression analyses were conducted to compare in-hospital mortality and to identify factors associated with clinical improvement or fatal outcomes. Results By day 10, more patients showed improvement with LPV/r and DRV/r (p=0.03 and 0.01, respectively), but only LPV/r was associated with improved survival compared to the control group (p=0.05). Factors associated with mortality included male gender (HR: 3.63, p=0.02), diabetes (HR: 2.49, p=0.03), oxygen saturation below 90% at admission (HR: 5.23, p<0.01), high blood glucose levels (HR: 3.68, p=0.01), age (HR: 1.04, p=0.02), and more than 25% lesion extension on chest CT scan (HR: 2.28, p=0.03). Conclusions LPV/r, but not DRV/r, showed a survival benefit in patients hospitalised with COVID-19, but these findings deserve further investigation in a randomised clinical trial.
Collapse
Affiliation(s)
- Dóra Paróczai
- Department of Medical Microbiology, University of Szeged, Szeged, Hungary
- Albert Szent-Györgyi Health Center, Pulmonology Clinic, University of Szeged, Deszk, Hungary
| | - András Bikov
- North West Lung Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
- Division of Immunology, Immunity to Infection and Respiratory Medicine, University of Manchester, Manchester, United Kingdom
| | - Andreea Blidaru
- Department of Infectious Diseases, Infectious Diseases and Pulmonology Clinical Hospital, Timisoara, Romania
| | - Emanuel Bobu
- Department of Pulmonology, University of Medicine and Pharmacy Timisoara, Timisoara, Romania
| | - Ana Lascu
- Department of Functional Sciences, Discipline of Pathophysiology, Centre for Translational Research and Systems Medicine, University of Medicine and Pharmacy Timisoara, Timisoara, Romania
- Institute for Cardiovascular Diseases of Timisoara, Clinic for Cardiovascular Surgery, Timisoara, Romania
| | - Cristian Ion Mot
- ENT Department, Municipal Emergency Hospital Timisoara, Timisoara, Romania
- Department of Surgery, University of Medicine and Pharmacy Timisoara, Timisoara, Romania
| | - Stefan Mihaicuta
- Department of Infectious Diseases, Infectious Diseases and Pulmonology Clinical Hospital, Timisoara, Romania
- Centre for Research and Innovation in Precision Medicine of Respiratory Diseases, Department of Pulmonology, University of Medicine and Pharmacy Timisoara, Timisoara, Romania
| | - Stefan Frent
- Department of Infectious Diseases, Infectious Diseases and Pulmonology Clinical Hospital, Timisoara, Romania
- Centre for Research and Innovation in Precision Medicine of Respiratory Diseases, Department of Pulmonology, University of Medicine and Pharmacy Timisoara, Timisoara, Romania
| |
Collapse
|
3
|
Arman BY, Brun J, Hill ML, Zitzmann N, von Delft A. An Update on SARS-CoV-2 Clinical Trial Results-What We Can Learn for the Next Pandemic. Int J Mol Sci 2023; 25:354. [PMID: 38203525 PMCID: PMC10779148 DOI: 10.3390/ijms25010354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/21/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has claimed over 7 million lives worldwide, providing a stark reminder of the importance of pandemic preparedness. Due to the lack of approved antiviral drugs effective against coronaviruses at the start of the pandemic, the world largely relied on repurposed efforts. Here, we summarise results from randomised controlled trials to date, as well as selected in vitro data of directly acting antivirals, host-targeting antivirals, and immunomodulatory drugs. Overall, repurposing efforts evaluating directly acting antivirals targeting other viral families were largely unsuccessful, whereas several immunomodulatory drugs led to clinical improvement in hospitalised patients with severe disease. In addition, accelerated drug discovery efforts during the pandemic progressed to multiple novel directly acting antivirals with clinical efficacy, including small molecule inhibitors and monoclonal antibodies. We argue that large-scale investment is required to prepare for future pandemics; both to develop an arsenal of broad-spectrum antivirals beyond coronaviruses and build worldwide clinical trial networks that can be rapidly utilised.
Collapse
Affiliation(s)
- Benediktus Yohan Arman
- Antiviral Drug Discovery Unit, Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (J.B.); (N.Z.)
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Juliane Brun
- Antiviral Drug Discovery Unit, Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (J.B.); (N.Z.)
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Michelle L. Hill
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK;
| | - Nicole Zitzmann
- Antiviral Drug Discovery Unit, Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (J.B.); (N.Z.)
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Annette von Delft
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
- Centre for Medicine Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| |
Collapse
|
4
|
Chaurasiya A, Shome A, Chawla PA. Molecular docking analysis of peptide-based antiviral agents against SARS-CoV-2 main protease: an approach towards drug repurposing. EXPLORATION OF MEDICINE 2023. [DOI: 10.37349/emed.2023.00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
Aim:
Utilizing the therapeutic potentials of previously approved medications against a new target or pharmacological response is known as drug repurposing. The health and scientific communities are under continual pressure to discover new compounds with antiviral potential due to the rising reports of viral resistance and the occurrence and re-emergence of viral outbreaks. The use of antiviral peptides has emerged as an intriguing option in this search. Here, this article includes the current United States Food and Drug Administration (FDA)-approved antiviral peptides that might be enforced for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and carried out docking study of the viral protease inhibitors.
Methods:
In silico techniques like molecular docking was carried out using Autodock Vina software.
Results:
The molecular docking studies of peptide-based antiviral agents against SARS-CoV-2 [Protein Data Bank (PDB) ID: 7P35] using docking software AutoDockTools 1.5.6. Among all the docked ligands, compound velpatasvir showed interaction with residues ILE213, GLN256, LEU141, GLN189, GLU166, HIS41, CYS145, and ASN142, and displayed the highest docking score of –8.2 kcal/mol. This medication could be a novel treatment lead or candidate for treating SARS-CoV-2.
Conclusions:
To conclude, a docking study of peptide based antiviral compounds for their binding mode in the catalytic domain of SARS-CoV-2 receptor is reported. On molecular docking, the compounds have showed remarkable binding affinity with the amino acids of receptor chain A. The compounds occupied the same binding cavity as the reference compound maintaining the interactions with conserved amino acid residues essential for significant inhibitory potential, especially for compound velpatasvir with binding score of –8.2 kcal/mol.
Collapse
Affiliation(s)
- Abhishek Chaurasiya
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142001, India
| | - Abhimannu Shome
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142001, India
| | - Pooja A. Chawla
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142001, India
| |
Collapse
|
5
|
Ceramella J, Iacopetta D, Sinicropi MS, Andreu I, Mariconda A, Saturnino C, Giuzio F, Longo P, Aquaro S, Catalano A. Drugs for COVID-19: An Update. Molecules 2022; 27:8562. [PMID: 36500655 PMCID: PMC9740261 DOI: 10.3390/molecules27238562] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was the seventh known human coronavirus, and it was identified in Wuhan, Hubei province, China, in 2020. It caused the highly contagious disease called coronavirus disease 2019 (COVID-19), declared a global pandemic by the World Health Organization (WHO) on 11 March 2020. A great number of studies in the search of new therapies and vaccines have been carried out in these three long years, producing a series of successes; however, the need for more effective vaccines, therapies and other solutions is still being pursued. This review represents a tracking shot of the current pharmacological therapies used for the treatment of COVID-19.
Collapse
Affiliation(s)
- Jessica Ceramella
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, 87036 Rende, Italy
| | - Domenico Iacopetta
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, 87036 Rende, Italy
| | - Maria Stefania Sinicropi
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, 87036 Rende, Italy
| | - Inmaculada Andreu
- Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
- Unidad Mixta de Investigación UPV-IIS La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026 Valencia, Spain
| | | | - Carmela Saturnino
- Department of Science, University of Basilicata, 85100 Potenza, Italy
| | - Federica Giuzio
- Department of Science, University of Basilicata, 85100 Potenza, Italy
| | - Pasquale Longo
- Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Stefano Aquaro
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, 87036 Rende, Italy
| | - Alessia Catalano
- Department of Pharmacy-Drug Sciences, University of Bari “Aldo Moro”, 70126 Bari, Italy
| |
Collapse
|
6
|
A Review of Potential Therapeutic Strategies for COVID-19. Viruses 2022; 14:v14112346. [PMID: 36366444 PMCID: PMC9696587 DOI: 10.3390/v14112346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 02/01/2023] Open
Abstract
Coronavirus disease 2019 is a rather heterogeneous disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The ongoing pandemic is a global threat with increasing death tolls worldwide. SARS-CoV-2 belongs to lineage B β-CoV, a subgroup of Sarbecovirus. These enveloped, large, positive-sense single-stranded RNA viruses are easily spread among individuals, mainly via the respiratory system and droplets. Although the disease has been gradually controlled in many countries, once social restrictions are relaxed the virus may rebound, leading to a more severe and uncontrollable situation again, as occurred in Shanghai, China, in 2022. The current global health threat calls for the urgent development of effective therapeutic options for the treatment and prevention of SARS-CoV-2 infection. This systematic overview of possible SARS-CoV-2 therapeutic strategies from 2019 to 2022 indicates three potential targets: virus entry, virus replication, and the immune system. The information provided in this review will aid the development of more potent and specific antiviral compounds.
Collapse
|