1
|
Ruiz-Moreno AJ, Cedillo-González R, Cordova-Bahena L, An Z, Medina-Franco JL, Velasco-Velázquez MA. Consensus Pharmacophore Strategy For Identifying Novel SARS-Cov-2 M pro Inhibitors from Large Chemical Libraries. J Chem Inf Model 2024; 64:1984-1995. [PMID: 38472094 PMCID: PMC10966741 DOI: 10.1021/acs.jcim.3c01439] [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: 09/10/2023] [Revised: 02/24/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main Protease (Mpro) is an enzyme that cleaves viral polyproteins translated from the viral genome and is critical for viral replication. Mpro is a target for anti-SARS-CoV-2 drug development, and multiple Mpro crystals complexed with competitive inhibitors have been reported. In this study, we aimed to develop an Mpro consensus pharmacophore as a tool to expand the search for inhibitors. We generated a consensus model by aligning and summarizing pharmacophoric points from 152 bioactive conformers of SARS-CoV-2 Mpro inhibitors. Validation against a library of conformers from a subset of ligands showed that our model retrieved poses that reproduced the crystal-binding mode in 77% of the cases. Using models derived from a consensus pharmacophore, we screened >340 million compounds. Pharmacophore-matching and chemoinformatics analyses identified new potential Mpro inhibitors. The candidate compounds were chemically dissimilar to the reference set, and among them, demonstrating the relevance of our model. We evaluated the effect of 16 candidates on Mpro enzymatic activity finding that seven have inhibitory activity. Three compounds (1, 4, and 5) had IC50 values in the midmicromolar range. The Mpro consensus pharmacophore reported herein can be used to identify compounds with improved activity and novel chemical scaffolds against Mpro. The method developed for its generation is provided as an open-access code (https://github.com/AngelRuizMoreno/ConcensusPharmacophore) and can be applied to other pharmacological targets.
Collapse
Affiliation(s)
- Angel J. Ruiz-Moreno
- School
of Medicine, Universidad Nacional Autónoma
de México, Mexico
City 04510, Mexico
| | - Raziel Cedillo-González
- School
of Medicine, Universidad Nacional Autónoma
de México, Mexico
City 04510, Mexico
- Graduate
Program in Biochemical Sciences, Universidad
Nacional Autónoma de México, Mexico City 04510, Mexico
- DIFACQUIM
Research Group, School of Chemistry, Universidad
Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Luis Cordova-Bahena
- School
of Medicine, Universidad Nacional Autónoma
de México, Mexico
City 04510, Mexico
- Consejo
Nacional de Humanidades, Ciencias y Tecnología, Mexico City 03940, Mexico
| | - Zhiqiang An
- Texas
Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - José L. Medina-Franco
- DIFACQUIM
Research Group, School of Chemistry, Universidad
Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Marco A. Velasco-Velázquez
- School
of Medicine, Universidad Nacional Autónoma
de México, Mexico
City 04510, Mexico
- Texas
Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas 77030, United States
| |
Collapse
|
2
|
Mottaghi A, Aryan Kya M. Spatial Proximity Distribution of COVID-19 in Iran (Panel: February 2019-February 2023). IRANIAN JOURNAL OF MEDICAL SCIENCES 2024; 49:62-64. [PMID: 38322158 PMCID: PMC10839143 DOI: 10.30476/ijms.2023.98665.3069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/28/2023] [Accepted: 07/14/2023] [Indexed: 02/08/2024]
Affiliation(s)
- Afshin Mottaghi
- Department of Political Geography, School of Geography Sciences, Kharazmi University, Tehran, Iran
| | - Michael Aryan Kya
- Department of Dentistry, School of Dentistry, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
3
|
Santos SJM, Valentini A. In silico investigation of Komaroviquinone as a potential inhibitor of SARS-CoV-2 main protease (Mpro): Molecular docking, molecular dynamics, and QM/MM approaches. J Mol Graph Model 2024; 126:108662. [PMID: 37950976 DOI: 10.1016/j.jmgm.2023.108662] [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: 07/20/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 11/13/2023]
Abstract
COVID-19 has highlighted the urgent need for new therapeutic agents to combat the spread of the virus. The main protease of SARS-CoV-2 (Mpro) has emerged as a promising target. In this study, we conducted an in silico investigation to explore the potential of Komaroviquinone, an icetexane diterpene, as a therapeutic agent against COVID-19. We employed molecular docking, molecular dynamics, and QM/MM methodologies to compare the binding affinity, molecular interactions, and stability of Komaroviquinone and the FDA-approved antiviral drug Nirmatrelvir with the SARS-CoV-2 Mpro protein. The study demonstrated that Komaroviquinone exhibits strong interaction with Mpro, with a binding energy comparable to Nirmatrelvir. The ADMET analysis revealed that Barbatusol, Brussonol, and Komaroviquinone possess superior solubility, permeability, and intestinal absorption compared to Nirmatrelvir, as well as more favorable distribution properties and lower toxicity profiles. Notably, Nirmatrelvir displayed toxicity and hepatotoxicity, which were not present in the natural compounds. Thus, it is suggested that Komaroviquinone may be a promising candidate for the development of effective and safer therapeutic agents against COVID-19. Experimental validation is necessary to confirm its potential as a treatment for the disease.
Collapse
Affiliation(s)
- Samuel J M Santos
- Federal Institute of Education, Science and Technology of Rio Grande Do Sul, 95770-000, Feliz, Rio Grande Do Sul, Brazil.
| | - Antoninho Valentini
- Department of Analytical Chemistry and Physical Chemistry, Federal University of Ceará, Campus of Pici, 60440-554, Fortaleza, Ceará, Brazil.
| |
Collapse
|
4
|
Leng A, Shah M, Ahmad SA, Premraj L, Wildi K, Li Bassi G, Pardo CA, Choi A, Cho SM. Pathogenesis Underlying Neurological Manifestations of Long COVID Syndrome and Potential Therapeutics. Cells 2023; 12:816. [PMID: 36899952 PMCID: PMC10001044 DOI: 10.3390/cells12050816] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/28/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
The development of long-term symptoms of coronavirus disease 2019 (COVID-19) more than four weeks after primary infection, termed "long COVID" or post-acute sequela of COVID-19 (PASC), can implicate persistent neurological complications in up to one third of patients and present as fatigue, "brain fog", headaches, cognitive impairment, dysautonomia, neuropsychiatric symptoms, anosmia, hypogeusia, and peripheral neuropathy. Pathogenic mechanisms of these symptoms of long COVID remain largely unclear; however, several hypotheses implicate both nervous system and systemic pathogenic mechanisms such as SARS-CoV2 viral persistence and neuroinvasion, abnormal immunological response, autoimmunity, coagulopathies, and endotheliopathy. Outside of the CNS, SARS-CoV-2 can invade the support and stem cells of the olfactory epithelium leading to persistent alterations to olfactory function. SARS-CoV-2 infection may induce abnormalities in innate and adaptive immunity including monocyte expansion, T-cell exhaustion, and prolonged cytokine release, which may cause neuroinflammatory responses and microglia activation, white matter abnormalities, and microvascular changes. Additionally, microvascular clot formation can occlude capillaries and endotheliopathy, due to SARS-CoV-2 protease activity and complement activation, can contribute to hypoxic neuronal injury and blood-brain barrier dysfunction, respectively. Current therapeutics target pathological mechanisms by employing antivirals, decreasing inflammation, and promoting olfactory epithelium regeneration. Thus, from laboratory evidence and clinical trials in the literature, we sought to synthesize the pathophysiological pathways underlying neurological symptoms of long COVID and potential therapeutics.
Collapse
Affiliation(s)
- Albert Leng
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Manuj Shah
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Syed Ameen Ahmad
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lavienraj Premraj
- Department of Neurology, Griffith University School of Medicine, Gold Coast, Brisbane, QLD 4215, Australia
- Critical Care Research Group, The Prince Charles Hospital, Brisbane, QLD 4032, Australia
| | - Karin Wildi
- Critical Care Research Group, The Prince Charles Hospital, Brisbane, QLD 4032, Australia
| | - Gianluigi Li Bassi
- Critical Care Research Group, The Prince Charles Hospital, Brisbane, QLD 4032, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD 4072, Australia
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia
- Intensive Care Unit, St Andrew’s War Memorial Hospital and the Wesley Hospital, Uniting Care Hospitals, Brisbane, QLD 4000, Australia
- Wesley Medical Research, Auchenflower, QLD 4066, Australia
| | - Carlos A. Pardo
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alex Choi
- Division of Neurosciences Critical Care, Department of Neurosurgery, UT Houston, Houston, TX 77030, USA
| | - Sung-Min Cho
- Divisions of Neurosciences Critical Care and Cardiac Surgery, Departments of Neurology, Surgery, Anesthesiology and Critical Care Medicine and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| |
Collapse
|
5
|
Paxlovid (Nirmatrelvir/Ritonavir): A new approach to Covid-19 therapy? Biomed Pharmacother 2023; 162:114367. [PMID: 37018987 PMCID: PMC9899776 DOI: 10.1016/j.biopha.2023.114367] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/22/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023] Open
Abstract
Despite the need for novel, effective therapeutics for the COVID-19 pandemic, no curative regimen is yet available, therefore patients are forced to rely on supportive and nonspecific therapies. Some SARS-CoV-2 proteins, like the 3C-like protease (3CLpro) or the major protease (Mpro), have been identified as promising targets for antiviral drugs. The Mpro has major a role in protein processing as well as pathogenesis of the virus, and could be a useful therapeutic target. The antiviral drug nirmatrelvir can keep SARS-CoV-2 from replicating through inhibiting Mpro. Nirmatrelvir was combined with another HIV protease inhibitor, ritonavir, to create Paxlovid (Nirmatrelvir/Ritonavir). The metabolizing enzyme cytochrome P450 3 A is inhibited by ritonavir to lengthen the half-life of nirmatrelvir, so rintonavir acts as a pharmacological enhancer. Nirmatrelvir exhibits potent antiviral activity against current coronavirus variants, despite significant alterations in the SARS-CoV-2 viral genome. Nevertheless, there are still several unanswered questions. This review summarizes the current literature on nirmatrelvir and ritonavir efficacy in treating SARS-CoV-2 infection, and also their safety and possible side effects.
Collapse
|