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Rut W, Groborz K, Sun X, Hilgenfeld R, Drag M. Profiling of coronaviral M pro and enteroviral 3C pro specificity provides a framework for the development of broad-spectrum antiviral compounds. Protein Sci 2024; 33:e5139. [PMID: 39150063 PMCID: PMC11328108 DOI: 10.1002/pro.5139] [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: 05/06/2024] [Revised: 07/04/2024] [Accepted: 07/20/2024] [Indexed: 08/17/2024]
Abstract
The main protease from coronaviruses and the 3C protease from enteroviruses play a crucial role in processing viral polyproteins, making them attractive targets for the development of antiviral agents. In this study, we employed a combinatorial chemistry approach-HyCoSuL-to compare the substrate specificity profiles of the main and 3C proteases from alphacoronaviruses, betacoronaviruses, and enteroviruses. The obtained data demonstrate that coronavirus Mpros exhibit overlapping substrate specificity in all binding pockets, whereas the 3Cpro from enterovirus displays slightly different preferences toward natural and unnatural amino acids at the P4-P2 positions. However, chemical tools such as substrates, inhibitors, and activity-based probes developed for SARS-CoV-2 Mpro can be successfully applied to investigate the activity of the Mpro from other coronaviruses as well as the 3Cpro from enteroviruses. Our study provides a structural framework for the development of broad-spectrum antiviral compounds.
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Affiliation(s)
- Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Katarzyna Groborz
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, Lübeck, Germany
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wroclaw, Poland
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2
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Dampalla CS, Kim Y, Zabiegala A, Howard DJ, Nguyen HN, Madden TK, Thurman HA, Cooper A, Liu L, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-Guided Design of Potent Coronavirus Inhibitors with a 2-Pyrrolidone Scaffold: Biochemical, Crystallographic, and Virological Studies. J Med Chem 2024; 67:11937-11956. [PMID: 38953866 DOI: 10.1021/acs.jmedchem.4c00551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Zoonotic coronaviruses are known to produce severe infections in humans and have been the cause of significant morbidity and mortality worldwide. SARS-CoV-2 was the largest and latest contributor of fatal cases, even though MERS-CoV has the highest case-fatality ratio among zoonotic coronaviruses. These infections pose a high risk to public health worldwide warranting efforts for the expeditious discovery of antivirals. Hence, we hereby describe a novel series of inhibitors of coronavirus 3CLpro embodying an N-substituted 2-pyrrolidone scaffold envisaged to exploit favorable interactions with the S3-S4 subsites and connected to an invariant Leu-Gln P2-P1 recognition element. Several inhibitors showed nanomolar antiviral activity in enzyme and cell-based assays, with no significant cytotoxicity. High-resolution crystal structures of inhibitors bound to the 3CLpro were determined to probe and identify the molecular determinants associated with binding, to inform the structure-guided optimization of the inhibitors, and to confirm the mechanism of action of the inhibitors.
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Affiliation(s)
- Chamandi S Dampalla
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - Alexandria Zabiegala
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - Dennis J Howard
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Harry Nhat Nguyen
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Trent K Madden
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Hayden A Thurman
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Anne Cooper
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Lijun Liu
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Kevin P Battaile
- NYX, New York Structural Biology Center, Upton, New York 11973, United States
| | - Scott Lovell
- Protein Structure and X-ray Crystallography Laboratory, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, United States
| | - William C Groutas
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
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3
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Sil BK, Jamiruddin MR, Paul PK, Aekwattanaphol N, Nakpheng T, Haq MA, Buatong W, Srichana T. Ascorbic acid as serine protease inhibitor in lung cancer cell line and human serum albumin. PLoS One 2024; 19:e0303706. [PMID: 39042609 PMCID: PMC11265676 DOI: 10.1371/journal.pone.0303706] [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: 12/16/2023] [Accepted: 04/30/2024] [Indexed: 07/25/2024] Open
Abstract
Serine proteases (SPs) are distributed among all living cells accounting for almost one-third of all proteases. Dysregulation of SPs during inflammation and/or infection can result in devastating consequences, such as skin and lung inflammation, neuroinflammation, arthritis, as well as metastasis of cancerous cells. Such activities are tightly regulated by various inhibitors known as serine protease inhibitors (SERPIN). The thermodynamic investigations previously revealed that L-ascorbic acid binds to trypsin more firmly than pepsin and the binding force of L-ascorbic acid is driven by hydrogen bonds and van der Waals forces. However, the physiochemical effects of such interaction on trypsin and/or pepsin have not yet been reported. Ascorbic acid, also known as vitamin C, is one of the essential nutrients and most common food supplements, fortificants, and preservatives. The aim of this study was to explore the inhibitory effects of ascorbic acid on serine proteases at various concentrations on the in-vitro digestion and/or hydrolysis of intercellular matrix of cell monolayer and human serum albumin (HSA). The inhibitory effects of ascorbic on trypsin are investigated by qualitative and quantitative analysis using SDS-PAGE imaging and NIH densitometric software. Upon the addition of ascorbic acid in both indicator systems, the detachment and/or dissociation of cell monolayer and the digestion of HSA were inhibited in the presence of EDTA-Trypsin. The inhibitory effect of ascorbic acid on the digestion of intercellular matrix and/or hydrolysis of HSA showed a dose-dependent trend until it reached the maximum extent of inhibition. At an equal concentration (2.5mg/mL) ascorbic acid and EDTA-Trypsin exhibited the most potent inhibitory effect on the in vitro digestion of protein either in the form of intercellular matrix in cell monolayer and/or HSA respectively. Overall, our results based on two indicator systems strongly indicate that ascorbic acid may function as a serine protease inhibitor (SERPIN) beyond other important functions.
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Affiliation(s)
- Bijon Kumar Sil
- Drug Delivery System Excellence Center, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Songkhla, Thailand
| | | | - Pijush Kumar Paul
- Drug Delivery System Excellence Center, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Songkhla, Thailand
| | - Nattanit Aekwattanaphol
- Drug Delivery System Excellence Center, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Songkhla, Thailand
| | - Titpawan Nakpheng
- Drug Delivery System Excellence Center, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Songkhla, Thailand
| | - Md. Ahsanul Haq
- Immunobiology, Nutrition and Toxicology Lab, Nutrition Research Division, icddr,b, Dhaka, Bangladesh
| | - Wilaiporn Buatong
- Drug Delivery System Excellence Center, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Songkhla, Thailand
| | - Teerapol Srichana
- Drug Delivery System Excellence Center, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Songkhla, Thailand
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4
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Song N, Zheng W, Song B, Zheng J. Allosteric Regulation and Inhibition of Coronavirus 3CLpro Revealed by HDX-MS. Chembiochem 2024; 25:e202400001. [PMID: 38720172 DOI: 10.1002/cbic.202400001] [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: 01/01/2024] [Revised: 05/03/2024] [Indexed: 07/03/2024]
Abstract
Coronavirus (CoV) infections have caused contagious and fatal respiratory diseases in humans worldwide. CoV 3-chymotrypsin-like proteases (3CLpro or Mpro) play an important role in viral maturation, and maintenance of their dimeric conformation is crucial for viral activity. Therefore, allosterically regulated dimerization of 3CLpro can be employed as a drug development target. Here, we investigated the allosteric regulatory mechanism of 3CLpro dimerization by using hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) technology. We found that the FLAG tag directly coupled to the N-finger of 3CLpro significantly increased HDX kinetics at the dimer interface, and 3CLpro transformed from a dimer to a monomer. The 3CLpro mutants of SARS-CoV-2, which are monomeric, also exhibited increased deuterium exchange. Binding of the allosteric inhibitor Gastrodenol to most betacoronavirus 3CLpros led to increased allosteric deuterium exchange, resulting in the monomeric conformation of the CoV 3CLpro upon binding. Molecular dynamics (MD) simulation analysis further indicated the molecular mechanism of action of Gastrodenol on CoV 3CLpro: binding of Gastrodenol to SARS-CoV-2 3CLpro destroyed the hydrogen bond in the dimer interface. These results suggest that Gastrodenol may be a potential broad-spectrum anti-betacoronavirus drug.
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Affiliation(s)
- Ning Song
- Immunological Disease Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, 201203, Shanghai, PR China
- University of Chinese Academy of Sciences, No. 1 Yanqihu East Rd, Huairou District, 101408, Beijing, PR China
| | - Wen Zheng
- CADD computer-aided protein Design Simulator, Hubei Yuanda Biotechnology Co., Ltd., Building B6, Optics Valley Biological City, Hongshan District, 430000, Wuhan, Hubei, PR China
| | - Bin Song
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, 227 South Chongqing Road, 200025, Shanghai, PR China
| | - Jie Zheng
- Immunological Disease Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, 201203, Shanghai, PR China
- University of Chinese Academy of Sciences, No. 1 Yanqihu East Rd, Huairou District, 101408, Beijing, PR China
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5
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Li Y, Lu SM, Wang JL, Yao HP, Liang LG. Progress in SARS-CoV-2, diagnostic and clinical treatment of COVID-19. Heliyon 2024; 10:e33179. [PMID: 39021908 PMCID: PMC11253070 DOI: 10.1016/j.heliyon.2024.e33179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 07/20/2024] Open
Abstract
Background Corona Virus Disease 2019(COVID-19)is a global pandemic novel coronavirus infection disease caused by Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2). Although rapid, large-scale testing plays an important role in patient management and slowing the spread of the disease. However, there has been no good and widely used drug treatment for infection and transmission of SARS-CoV-2. Key findings Therefore, this review updates the body of knowledge on viral structure, infection routes, detection methods, and clinical treatment, with the aim of responding to the large-section caused by SARS-CoV-2. This paper focuses on the structure of SARS-CoV-2 viral protease, RNA polymerase, serine protease and main proteinase-like protease as well as targeted antiviral drugs. Conclusion In vitro or clinical trials have been carried out to provide deeper thinking for the pathogenesis, clinical diagnosis, vaccine development and treatment of SARS-CoV-2.
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Affiliation(s)
- Yang Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Si-Ming Lu
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Key Laboratory of Clinical in Vitro Diagnostic Techniques, Hangzhou, China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Jia-Long Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hang-Ping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Li-Guo Liang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Centre for Clinical Laboratory, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
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6
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Chatterjee AK. Discovery of novel anti-infective agents. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2024; 100:39-117. [PMID: 39034055 DOI: 10.1016/bs.apha.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Academic and other non-profit institutions have a long-term vision to improve human health where commercial interests can be limited for profit organizations. Medicinal chemistry to these diseases with no commercial benefit needs is well suited in the academic environment and this chapter outlines some work conducted at Calibr-Skaggs around antibiotic drug development that has led to initiation of multiple clinical trials over the last decade.
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Affiliation(s)
- Arnab K Chatterjee
- Calibr-Skaggs Institute of Innovation Medicines, Scripps Research, La Jolla, CA, United States.
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7
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Xiao YQ, Long J, Zhang SS, Zhu YY, Gu SX. Non-peptidic inhibitors targeting SARS-CoV-2 main protease: A review. Bioorg Chem 2024; 147:107380. [PMID: 38636432 DOI: 10.1016/j.bioorg.2024.107380] [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: 02/20/2024] [Revised: 04/11/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024]
Abstract
The COVID-19 pandemic continues to pose a threat to global health, and sounds the alarm for research & development of effective anti-coronavirus drugs, which are crucial for the patients and urgently needed for the current epidemic and future crisis. The main protease (Mpro) stands as an essential enzyme in the maturation process of SARS-CoV-2, playing an irreplaceable role in regulating viral RNA replication and transcription. It has emerged as an ideal target for developing antiviral agents against SARS-CoV-2 due to its high conservation and the absence of homologous proteases in the human body. Among the SARS-CoV-2 Mpro inhibitors, non-peptidic compounds hold promising prospects owing to their excellent antiviral activity and improved metabolic stability. In this review, we offer an overview of research progress concerning non-peptidic SARS-CoV-2 Mpro inhibitors since 2020. The efforts delved into molecular structures, structure-activity relationships (SARs), biological activity, and binding modes of these inhibitors with Mpro. This review aims to provide valuable clues and insights for the development of anti-SARS-CoV-2 agents as well as broad-spectrum coronavirus Mpro inhibitors.
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Affiliation(s)
- Ya-Qi Xiao
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China
| | - Jiao Long
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China
| | - Shuang-Shuang Zhang
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Yuan-Yuan Zhu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Shuang-Xi Gu
- School of Chemical Engineering and Pharmacy, Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China.
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Nazir MS, Ahmad M, Aslam S, Rafiq A, Al-Hussain SA, Zaki MEA. A Comprehensive Update of Anti-COVID-19 Activity of Heterocyclic Compounds. Drug Des Devel Ther 2024; 18:1547-1571. [PMID: 38737333 PMCID: PMC11088867 DOI: 10.2147/dddt.s450499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/24/2024] [Indexed: 05/14/2024] Open
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic is one of the most considerable health problems across the world. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the major causative agent of COVID-19. The severe symptoms of this deadly disease include shortness of breath, fever, cough, loss of smell, and a broad spectrum of other health issues such as diarrhea, pneumonia, bronchitis, septic shock, and multiple organ failure. Currently, there are no medications available for coronavirus patients, except symptom-relieving drugs. Therefore, SARS-CoV-2 requires the development of effective drugs and specific treatments. Heterocycles are important constituents of more than 85% of the physiologically active pharmaceutical drugs on the market now. Several FDA-approved drugs have been reported including molnupiravir, remdesivir, ritonavir, oseltamivir, favipiravir, chloroquine, and hydroxychloroquine for the cure of COVID-19. In this study, we discuss potent anti-SARS-CoV-2 heterocyclic compounds that have been synthesized over the past few years. These compounds included; indole, piperidine, pyrazine, pyrimidine, pyrrole, piperazine, quinazoline, oxazole, quinoline, isoxazole, thiazole, quinoxaline, pyrazole, azafluorene, imidazole, thiadiazole, triazole, coumarin, chromene, and benzodioxole. Both in vitro and in silico studies were performed to determine the potential of these heterocyclic compounds in the fight against various SARS-CoV-2 proteins.
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Affiliation(s)
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad, Pakistan
| | - Sana Aslam
- Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Ayesha Rafiq
- Department of Chemistry, Government College University, Faisalabad, Pakistan
| | - Sami A Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Magdi E A Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
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Saheb Sharif-Askari F, Ali Hussain Alsayed H, Saheb Sharif-Askari N, Saddik B, Al Sayed Hussain A, Halwani R. Risk factors and early preventive measures for long COVID in non-hospitalized patients: analysis of a large cohort in the United Arab Emirates. Public Health 2024; 230:198-206. [PMID: 38574425 DOI: 10.1016/j.puhe.2024.02.031] [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: 07/06/2023] [Revised: 02/07/2024] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
OBJECTIVES Long COVID is characterized by persistent symptoms lasting for 4 weeks or more following the acute infection with SARS-CoV-2. Risk factors for long COVID and the impact of pre-COVID vaccination and treatment during acute COVID-19 remain uncertain. This study aimed to investigate patient-specific factors associated with long COVID in a large cohort of non-hospitalized adult patients with mild to moderate COVID-19 in Dubai. STUDY DESIGN Cohort study. METHODS The study included 28,375 non-hospitalized adult patients diagnosed with mild to moderate COVID-19 between January 1, 2021, and September 31, 2022, in Dubai, who were followed up for 90 days. The presence of long COVID symptoms was documented by physicians during patient visits to the family medicine department. Furthermore, long COVID-related risk factors were collected and analyzed, including patient demographics, comorbidities, pre-COVID vaccination status, and the COVID-related treatments received during the acute phase of the illness. Cox proportional hazard models were applied for the statistical analysis. RESULTS Among the cohort, 2.8% of patients experienced long COVID symptoms during the 90-day follow-up. Patients with long COVID tended to be younger, female, and of Caucasian race. Common symptoms included fatigue, muscle pain, respiratory symptoms, abdominal and neurological symptoms, allergic reactions, skin rashes, and hair loss. Risk factors for long COVID were identified as diabetes mellitus, asthma, and Vitamin D deficiency. Females and Caucasians had a higher risk of long COVID during the pre-Omicron period compared to the Omicron period. Pre-COVID vaccination was associated with a reduced risk of long COVID in all patient subgroups. Treatment with favipiravir or sotrovimab during the acute phase of COVID-19 was linked to a decreased risk of long COVID, although favipiravir showed limited effectiveness in the high-risk group. CONCLUSION This study contributes to the existing knowledge by identifying risk factors for long COVID among non-hospitalized patients and emphasizing the potential benefits of pre-COVID vaccination and timely treatment.
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Affiliation(s)
- Fatemeh Saheb Sharif-Askari
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates; Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Hawra Ali Hussain Alsayed
- Department of Pharmacy, Rashid Hospital, Dubai Academic Health Corporation, Dubai, United Arab Emirates
| | - Narjes Saheb Sharif-Askari
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates; Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Basema Saddik
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates; Department of Family and Community Medicine, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates; School of Population Health, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Ali Al Sayed Hussain
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Rabih Halwani
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates; Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates; Prince Abdullah Ben Khaled Celiac Disease Chair, Department of Pediatrics, Faculty of Medicine, King Saud University, Saudi Arabia.
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10
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Azevedo PHRDA, Camargo PG, Constant LEC, Costa SDS, Silva CS, Rosa AS, Souza DDC, Tucci AR, Ferreira VNS, Oliveira TKF, Borba NRR, Rodrigues CR, Albuquerque MG, Dias LRS, Garrett R, Miranda MD, Allonso D, Lima CHDS, Muri EMF. Statine-based peptidomimetic compounds as inhibitors for SARS-CoV-2 main protease (SARS-CoV‑2 Mpro). Sci Rep 2024; 14:8991. [PMID: 38637583 PMCID: PMC11026380 DOI: 10.1038/s41598-024-59442-4] [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: 10/26/2023] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
COVID-19 is a multisystemic disease caused by the SARS-CoV-2 airborne virus, a member of the Coronaviridae family. It has a positive sense single-stranded RNA genome and encodes two non-structural proteins through viral cysteine-proteases processing. Blocking this step is crucial to control virus replication. In this work, we reported the synthesis of 23 statine-based peptidomimetics to determine their ability to inhibit the main protease (Mpro) activity of SARS-CoV-2. Among the 23 peptidomimetics, 15 compounds effectively inhibited Mpro activity by 50% or more, while three compounds (7d, 8e, and 9g) exhibited maximum inhibition above 70% and IC50 < 1 µM. Compounds 7d, 8e, and 9g inhibited roughly 80% of SARS-CoV-2 replication and proved no cytotoxicity. Molecular docking simulations show putative hydrogen bond and hydrophobic interactions between specific amino acids and these inhibitors. Molecular dynamics simulations further confirmed the stability and persisting interactions in Mpro's subsites, exhibiting favorable free energy binding (ΔGbind) values. These findings suggest the statine-based peptidomimetics as potential therapeutic agents against SARS-CoV-2 by targeting Mpro.
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Affiliation(s)
- Pedro Henrique R de A Azevedo
- Laboratório de Química Medicinal, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, 24241-000, Brazil
| | - Priscila G Camargo
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Larissa E C Constant
- Laboratório de Biotecnologia e Bioengenharia Tecidual, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Stephany da S Costa
- Laboratório de Biotecnologia e Bioengenharia Tecidual, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Celimar Sinézia Silva
- Laboratório de Biotecnologia e Bioengenharia Tecidual, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Alice S Rosa
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Daniel D C Souza
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Amanda R Tucci
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Vivian N S Ferreira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Thamara Kelcya F Oliveira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Nathalia R R Borba
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Carlos R Rodrigues
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Magaly G Albuquerque
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Luiza R S Dias
- Laboratório de Química Medicinal, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, 24241-000, Brazil
| | - Rafael Garrett
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Milene D Miranda
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Diego Allonso
- Laboratório de Biotecnologia e Bioengenharia Tecidual, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
- Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil
| | - Camilo Henrique da S Lima
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-853, Brazil.
| | - Estela Maris F Muri
- Laboratório de Química Medicinal, Faculdade de Farmácia, Universidade Federal Fluminense, Niterói, RJ, 24241-000, Brazil.
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11
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Hammond J, Fountaine RJ, Yunis C, Fleishaker D, Almas M, Bao W, Wisemandle W, Baniecki ML, Hendrick VM, Kalfov V, Simón-Campos JA, Pypstra R, Rusnak JM. Nirmatrelvir for Vaccinated or Unvaccinated Adult Outpatients with Covid-19. N Engl J Med 2024; 390:1186-1195. [PMID: 38598573 PMCID: PMC11156287 DOI: 10.1056/nejmoa2309003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
BACKGROUND Nirmatrelvir in combination with ritonavir is an antiviral treatment for mild-to-moderate coronavirus disease 2019 (Covid-19). The efficacy of this treatment in patients who are at standard risk for severe Covid-19 or who are fully vaccinated and have at least one risk factor for severe Covid-19 has not been established. METHODS In this phase 2-3 trial, we randomly assigned adults who had confirmed Covid-19 with symptom onset within the past 5 days in a 1:1 ratio to receive nirmatrelvir-ritonavir or placebo every 12 hours for 5 days. Patients who were fully vaccinated against Covid-19 and who had at least one risk factor for severe disease, as well as patients without such risk factors who had never been vaccinated against Covid-19 or had not been vaccinated within the previous year, were eligible for participation. Participants logged the presence and severity of prespecified Covid-19 signs and symptoms daily from day 1 through day 28. The primary end point was the time to sustained alleviation of all targeted Covid-19 signs and symptoms. Covid-19-related hospitalization and death from any cause were also assessed through day 28. RESULTS Among the 1296 participants who underwent randomization and were included in the full analysis population, 1288 received at least one dose of nirmatrelvir-ritonavir (654 participants) or placebo (634 participants) and had at least one postbaseline visit. The median time to sustained alleviation of all targeted signs and symptoms of Covid-19 was 12 days in the nirmatrelvir-ritonavir group and 13 days in the placebo group (P = 0.60). Five participants (0.8%) in the nirmatrelvir-ritonavir group and 10 (1.6%) in the placebo group were hospitalized for Covid-19 or died from any cause (difference, -0.8 percentage points; 95% confidence interval, -2.0 to 0.4). The percentages of participants with adverse events were similar in the two groups (25.8% with nirmatrelvir-ritonavir and 24.1% with placebo). In the nirmatrelvir-ritonavir group, the most commonly reported treatment-related adverse events were dysgeusia (in 5.8% of the participants) and diarrhea (in 2.1%). CONCLUSIONS The time to sustained alleviation of all signs and symptoms of Covid-19 did not differ significantly between participants who received nirmatrelvir-ritonavir and those who received placebo. (Supported by Pfizer; EPIC-SR ClinicalTrials.gov number, NCT05011513.).
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Affiliation(s)
- Jennifer Hammond
- From Global Product Development, Pfizer, Collegeville, PA (J.H.); Global Product Development, Pfizer, Groton, CT (R.J.F.); Global Product Development, Pfizer, Lake Mary (C.Y.), and Global Product Development, Pfizer, Tampa (J.M.R.) - both in Florida; Global Product Development, Pfizer, Lexington, KY (D.F.); Global Product Development, Pfizer, New York (M.A., W.B., R.P.); Global Product Development, Pfizer, Lake Forest, IL (W.W.); Early Clinical Development, Pfizer, Cambridge, MA (M.L.B.); Pfizer, Sandwich, United Kingdom (V.M.H.); the Specialized Hospital for Active Treatment of Pneumo-Phthisiatric Diseases, Haskovo, Bulgaria (V.K.); and Méchnikov Project, Köhler and Milstein Research, Anahuac-Mayab University, Mérida, Mexico (J.A.S.-C.)
| | - Robert J Fountaine
- From Global Product Development, Pfizer, Collegeville, PA (J.H.); Global Product Development, Pfizer, Groton, CT (R.J.F.); Global Product Development, Pfizer, Lake Mary (C.Y.), and Global Product Development, Pfizer, Tampa (J.M.R.) - both in Florida; Global Product Development, Pfizer, Lexington, KY (D.F.); Global Product Development, Pfizer, New York (M.A., W.B., R.P.); Global Product Development, Pfizer, Lake Forest, IL (W.W.); Early Clinical Development, Pfizer, Cambridge, MA (M.L.B.); Pfizer, Sandwich, United Kingdom (V.M.H.); the Specialized Hospital for Active Treatment of Pneumo-Phthisiatric Diseases, Haskovo, Bulgaria (V.K.); and Méchnikov Project, Köhler and Milstein Research, Anahuac-Mayab University, Mérida, Mexico (J.A.S.-C.)
| | - Carla Yunis
- From Global Product Development, Pfizer, Collegeville, PA (J.H.); Global Product Development, Pfizer, Groton, CT (R.J.F.); Global Product Development, Pfizer, Lake Mary (C.Y.), and Global Product Development, Pfizer, Tampa (J.M.R.) - both in Florida; Global Product Development, Pfizer, Lexington, KY (D.F.); Global Product Development, Pfizer, New York (M.A., W.B., R.P.); Global Product Development, Pfizer, Lake Forest, IL (W.W.); Early Clinical Development, Pfizer, Cambridge, MA (M.L.B.); Pfizer, Sandwich, United Kingdom (V.M.H.); the Specialized Hospital for Active Treatment of Pneumo-Phthisiatric Diseases, Haskovo, Bulgaria (V.K.); and Méchnikov Project, Köhler and Milstein Research, Anahuac-Mayab University, Mérida, Mexico (J.A.S.-C.)
| | - Dona Fleishaker
- From Global Product Development, Pfizer, Collegeville, PA (J.H.); Global Product Development, Pfizer, Groton, CT (R.J.F.); Global Product Development, Pfizer, Lake Mary (C.Y.), and Global Product Development, Pfizer, Tampa (J.M.R.) - both in Florida; Global Product Development, Pfizer, Lexington, KY (D.F.); Global Product Development, Pfizer, New York (M.A., W.B., R.P.); Global Product Development, Pfizer, Lake Forest, IL (W.W.); Early Clinical Development, Pfizer, Cambridge, MA (M.L.B.); Pfizer, Sandwich, United Kingdom (V.M.H.); the Specialized Hospital for Active Treatment of Pneumo-Phthisiatric Diseases, Haskovo, Bulgaria (V.K.); and Méchnikov Project, Köhler and Milstein Research, Anahuac-Mayab University, Mérida, Mexico (J.A.S.-C.)
| | - Mary Almas
- From Global Product Development, Pfizer, Collegeville, PA (J.H.); Global Product Development, Pfizer, Groton, CT (R.J.F.); Global Product Development, Pfizer, Lake Mary (C.Y.), and Global Product Development, Pfizer, Tampa (J.M.R.) - both in Florida; Global Product Development, Pfizer, Lexington, KY (D.F.); Global Product Development, Pfizer, New York (M.A., W.B., R.P.); Global Product Development, Pfizer, Lake Forest, IL (W.W.); Early Clinical Development, Pfizer, Cambridge, MA (M.L.B.); Pfizer, Sandwich, United Kingdom (V.M.H.); the Specialized Hospital for Active Treatment of Pneumo-Phthisiatric Diseases, Haskovo, Bulgaria (V.K.); and Méchnikov Project, Köhler and Milstein Research, Anahuac-Mayab University, Mérida, Mexico (J.A.S.-C.)
| | - Weihang Bao
- From Global Product Development, Pfizer, Collegeville, PA (J.H.); Global Product Development, Pfizer, Groton, CT (R.J.F.); Global Product Development, Pfizer, Lake Mary (C.Y.), and Global Product Development, Pfizer, Tampa (J.M.R.) - both in Florida; Global Product Development, Pfizer, Lexington, KY (D.F.); Global Product Development, Pfizer, New York (M.A., W.B., R.P.); Global Product Development, Pfizer, Lake Forest, IL (W.W.); Early Clinical Development, Pfizer, Cambridge, MA (M.L.B.); Pfizer, Sandwich, United Kingdom (V.M.H.); the Specialized Hospital for Active Treatment of Pneumo-Phthisiatric Diseases, Haskovo, Bulgaria (V.K.); and Méchnikov Project, Köhler and Milstein Research, Anahuac-Mayab University, Mérida, Mexico (J.A.S.-C.)
| | - Wayne Wisemandle
- From Global Product Development, Pfizer, Collegeville, PA (J.H.); Global Product Development, Pfizer, Groton, CT (R.J.F.); Global Product Development, Pfizer, Lake Mary (C.Y.), and Global Product Development, Pfizer, Tampa (J.M.R.) - both in Florida; Global Product Development, Pfizer, Lexington, KY (D.F.); Global Product Development, Pfizer, New York (M.A., W.B., R.P.); Global Product Development, Pfizer, Lake Forest, IL (W.W.); Early Clinical Development, Pfizer, Cambridge, MA (M.L.B.); Pfizer, Sandwich, United Kingdom (V.M.H.); the Specialized Hospital for Active Treatment of Pneumo-Phthisiatric Diseases, Haskovo, Bulgaria (V.K.); and Méchnikov Project, Köhler and Milstein Research, Anahuac-Mayab University, Mérida, Mexico (J.A.S.-C.)
| | - Mary Lynn Baniecki
- From Global Product Development, Pfizer, Collegeville, PA (J.H.); Global Product Development, Pfizer, Groton, CT (R.J.F.); Global Product Development, Pfizer, Lake Mary (C.Y.), and Global Product Development, Pfizer, Tampa (J.M.R.) - both in Florida; Global Product Development, Pfizer, Lexington, KY (D.F.); Global Product Development, Pfizer, New York (M.A., W.B., R.P.); Global Product Development, Pfizer, Lake Forest, IL (W.W.); Early Clinical Development, Pfizer, Cambridge, MA (M.L.B.); Pfizer, Sandwich, United Kingdom (V.M.H.); the Specialized Hospital for Active Treatment of Pneumo-Phthisiatric Diseases, Haskovo, Bulgaria (V.K.); and Méchnikov Project, Köhler and Milstein Research, Anahuac-Mayab University, Mérida, Mexico (J.A.S.-C.)
| | - Victoria M Hendrick
- From Global Product Development, Pfizer, Collegeville, PA (J.H.); Global Product Development, Pfizer, Groton, CT (R.J.F.); Global Product Development, Pfizer, Lake Mary (C.Y.), and Global Product Development, Pfizer, Tampa (J.M.R.) - both in Florida; Global Product Development, Pfizer, Lexington, KY (D.F.); Global Product Development, Pfizer, New York (M.A., W.B., R.P.); Global Product Development, Pfizer, Lake Forest, IL (W.W.); Early Clinical Development, Pfizer, Cambridge, MA (M.L.B.); Pfizer, Sandwich, United Kingdom (V.M.H.); the Specialized Hospital for Active Treatment of Pneumo-Phthisiatric Diseases, Haskovo, Bulgaria (V.K.); and Méchnikov Project, Köhler and Milstein Research, Anahuac-Mayab University, Mérida, Mexico (J.A.S.-C.)
| | - Veselin Kalfov
- From Global Product Development, Pfizer, Collegeville, PA (J.H.); Global Product Development, Pfizer, Groton, CT (R.J.F.); Global Product Development, Pfizer, Lake Mary (C.Y.), and Global Product Development, Pfizer, Tampa (J.M.R.) - both in Florida; Global Product Development, Pfizer, Lexington, KY (D.F.); Global Product Development, Pfizer, New York (M.A., W.B., R.P.); Global Product Development, Pfizer, Lake Forest, IL (W.W.); Early Clinical Development, Pfizer, Cambridge, MA (M.L.B.); Pfizer, Sandwich, United Kingdom (V.M.H.); the Specialized Hospital for Active Treatment of Pneumo-Phthisiatric Diseases, Haskovo, Bulgaria (V.K.); and Méchnikov Project, Köhler and Milstein Research, Anahuac-Mayab University, Mérida, Mexico (J.A.S.-C.)
| | - J Abraham Simón-Campos
- From Global Product Development, Pfizer, Collegeville, PA (J.H.); Global Product Development, Pfizer, Groton, CT (R.J.F.); Global Product Development, Pfizer, Lake Mary (C.Y.), and Global Product Development, Pfizer, Tampa (J.M.R.) - both in Florida; Global Product Development, Pfizer, Lexington, KY (D.F.); Global Product Development, Pfizer, New York (M.A., W.B., R.P.); Global Product Development, Pfizer, Lake Forest, IL (W.W.); Early Clinical Development, Pfizer, Cambridge, MA (M.L.B.); Pfizer, Sandwich, United Kingdom (V.M.H.); the Specialized Hospital for Active Treatment of Pneumo-Phthisiatric Diseases, Haskovo, Bulgaria (V.K.); and Méchnikov Project, Köhler and Milstein Research, Anahuac-Mayab University, Mérida, Mexico (J.A.S.-C.)
| | - Rienk Pypstra
- From Global Product Development, Pfizer, Collegeville, PA (J.H.); Global Product Development, Pfizer, Groton, CT (R.J.F.); Global Product Development, Pfizer, Lake Mary (C.Y.), and Global Product Development, Pfizer, Tampa (J.M.R.) - both in Florida; Global Product Development, Pfizer, Lexington, KY (D.F.); Global Product Development, Pfizer, New York (M.A., W.B., R.P.); Global Product Development, Pfizer, Lake Forest, IL (W.W.); Early Clinical Development, Pfizer, Cambridge, MA (M.L.B.); Pfizer, Sandwich, United Kingdom (V.M.H.); the Specialized Hospital for Active Treatment of Pneumo-Phthisiatric Diseases, Haskovo, Bulgaria (V.K.); and Méchnikov Project, Köhler and Milstein Research, Anahuac-Mayab University, Mérida, Mexico (J.A.S.-C.)
| | - James M Rusnak
- From Global Product Development, Pfizer, Collegeville, PA (J.H.); Global Product Development, Pfizer, Groton, CT (R.J.F.); Global Product Development, Pfizer, Lake Mary (C.Y.), and Global Product Development, Pfizer, Tampa (J.M.R.) - both in Florida; Global Product Development, Pfizer, Lexington, KY (D.F.); Global Product Development, Pfizer, New York (M.A., W.B., R.P.); Global Product Development, Pfizer, Lake Forest, IL (W.W.); Early Clinical Development, Pfizer, Cambridge, MA (M.L.B.); Pfizer, Sandwich, United Kingdom (V.M.H.); the Specialized Hospital for Active Treatment of Pneumo-Phthisiatric Diseases, Haskovo, Bulgaria (V.K.); and Méchnikov Project, Köhler and Milstein Research, Anahuac-Mayab University, Mérida, Mexico (J.A.S.-C.)
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12
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Zhang Y, Guo J, Liu Y, Qu Y, Li YQ, Mu Y, Li W. An allosteric mechanism for potent inhibition of SARS-CoV-2 main proteinase. Int J Biol Macromol 2024; 265:130644. [PMID: 38462102 DOI: 10.1016/j.ijbiomac.2024.130644] [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: 10/26/2023] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024]
Abstract
The main proteinase (Mpro) of SARS-CoV-2 plays a critical role in cleaving viral polyproteins into functional proteins required for viral replication and assembly, making it a prime drug target for COVID-19. It is well known that noncompetitive inhibition offers potential therapeutic options for treating COVID-19, which can effectively reduce the likelihood of cross-reactivity with other proteins and increase the selectivity of the drug. Therefore, the discovery of allosteric sites of Mpro has both scientific and practical significance. In this study, we explored the binding characteristics and inhibiting process of Mpro activity by two recently reported allosteric inhibitors, pelitinib and AT7519 which were obtained by the X-ray screening experiments, to probe the allosteric mechanism via molecular dynamic (MD) simulations. We found that pelitinib and AT7519 can stably bind to Mpro far from the active site. The binding affinity is estimated to be -24.37 ± 4.14 and - 26.96 ± 4.05 kcal/mol for pelitinib and AT7519, respectively, which is considerably stable compared with orthosteric drugs. Furthermore, the strong binding caused clear changes in the catalytic site of Mpro, thus decreasing the substrate accessibility. The community network analysis also validated that pelitinib and AT7519 strengthened intra- and inter-domain communication of Mpro dimer, resulting in a rigid Mpro, which could negatively impact substrate binding. In summary, our findings provide the detailed working mechanism for the two experimentally observed allosteric sites of Mpro. These allosteric sites greatly enhance the 'druggability' of Mpro and represent attractive targets for the development of new Mpro inhibitors.
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Affiliation(s)
- Yunju Zhang
- School of Physics, Shandong University, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, 999078, Macao
| | - Yang Liu
- School of Physics, Shandong University, China
| | - Yuanyuan Qu
- School of Physics, Shandong University, China
| | | | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Weifeng Li
- School of Physics, Shandong University, China.
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13
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Zengin IN, Koca MS, Tayfuroglu O, Yildiz M, Kocak A. Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 M pro. J Comput Aided Mol Des 2024; 38:15. [PMID: 38532176 DOI: 10.1007/s10822-024-00554-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024]
Abstract
Here, we introduce the use of ANI-ML potentials as a rescoring function in the host-guest interaction in molecular docking. Our results show that the "docking power" of ANI potentials can compete with the current scoring functions at the same level of computational cost. Benchmarking studies on CASF-2016 dataset showed that ANI is ranked in the top 5 scoring functions among the other 34 tested. In particular, the ANI predicted interaction energies when used in conjunction with GOLD-PLP scoring function can boost the top ranked solution to be the closest to the x-ray structure. Rapid and accurate calculation of interaction energies between ligand and protein also enables screening of millions of drug candidates/docking poses. Using a unique protocol in which docking by GOLD-PLP, rescoring by ANI-ML potentials and extensive MD simulations along with end state free energy methods are combined, we have screened FDA approved drugs against the SARS-CoV-2 main protease (Mpro). The top six drug molecules suggested by the consensus of these free energy methods have already been in clinical trials or proposed as potential drug molecules in previous theoretical and experimental studies, approving the validity and the power of accuracy in our screening method.
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Affiliation(s)
- Irem N Zengin
- Department of Chemistry, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - M Serdar Koca
- Department of Molecular Biology and Genetics, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
- Pfizer - Universidad de Granada - Junta de Andalucía Centre for Genomics and Oncological Research (GENYO), 18016, Granada, Spain
| | - Omer Tayfuroglu
- Department of Chemistry, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Muslum Yildiz
- Department of Molecular Biology and Genetics, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Abdulkadir Kocak
- Department of Chemistry, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey.
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14
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Ibrahim M, Sun X, de Oliveira VM, Liu R, Clayton J, Kilani HE, Shen J, Hilgenfeld R. Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study of the free enzyme and its complex with inhibitor 13b-K. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583178. [PMID: 38496596 PMCID: PMC10942327 DOI: 10.1101/2024.03.04.583178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
During the continuing evolution of SARS-CoV-2, the Omicron variant of concern emerged in the second half of 2021 and has been dominant since November that year. Along with its sublineages, it has maintained a prominent role ever since. The Nsp5 main protease (Mpro) of the Omicron virus is characterized by a single dominant mutation, P132H. Here we determined the X-ray crystal structures of the P132H mutant (or O-Mpro) as free enzyme and in complex with the Mpro inhibitor, the alpha-ketoamide 13b-K, and we conducted enzymology, biophysical as well as theoretical studies to characterize the O-Mpro. We found that O-Mpro has a similar overall structure and binding with 13b-K; however, it displays lower enzymatic activity and lower thermal stability compared to the WT-Mpro (with "WT" referring to the original Wuhan-1 strain). Intriguingly, the imidazole ring of His132 and the carboxylate plane of Glu240 are in a stacked configuration in the X-ray structures determined here. The empirical folding free energy calculations suggest that the O-Mpro dimer is destabilized relative to the WT-Mpro due to the less favorable van der Waals interactions and backbone conformation in the individual protomers. The all-atom continuous constant pH molecular dynamics (MD) simulations reveal that His132 and Glu240 display coupled titration. At pH 7, His132 is predominantly neutral and in a stacked configuration with respect to Glu240 which is charged. In order to examine whether the Omicron mutation eases the emergence of further Mpro mutations, we also determined crystal structures of the relatively frequent P132H+T169S double mutant but found little evidence for a correlation between the two sites.
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Affiliation(s)
- Mohamed Ibrahim
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Vinicius Martins de Oliveira
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Ruibin Liu
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Joseph Clayton
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Haifa El Kilani
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research (DZIF), Hamburg - Lübeck - Borstel - Riems Site, University of Lübeck, 23562 Lübeck, Germany
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15
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Biswas S, Mita MA, Afrose S, Hasan MR, Shimu MSS, Zaman S, Saleh MA. An in silico approach to develop potential therapies against Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Heliyon 2024; 10:e25837. [PMID: 38379969 PMCID: PMC10877303 DOI: 10.1016/j.heliyon.2024.e25837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/22/2024] Open
Abstract
A deadly respiratory disease Middle East Respiratory Syndrome (MERS) is caused by a perilous virus known as MERS-CoV, which has a severe impact on human health. Currently, there is no approved vaccine, prophylaxis, or antiviral therapeutics for preventing MERS-CoV infection. Due to its inexorable and integral role in the maturation and replication of the MERS-CoV virus, the 3C-like protease is unavoidly a viable therapeutic target. In this study, 2369 phytoconstituents were enlisted from Japanese medicinal plants, and these compounds were screened against 3C-like protease to identify feasible inhibitors. The best three compounds were identified as Kihadanin B, Robustaflavone, and 3-beta-O- (trans-p-Coumaroyl) maslinic acid, with binding energies of -9.8, -9.4, and -9.2 kcal/mol, respectively. The top three potential candidates interacted with several active site residues in the targeted protein, including Cys145, Met168, Glu169, Ala171, and Gln192. The best three compounds were assessed by in silico technique to determine their drug-likeness properties, and they exhibited the least harmful features and the greatest drug-like qualities. Various descriptors, such as solvent-accessible surface area, root-mean-square fluctuation, root-mean-square deviation, hydrogen bond, and radius of gyration, validated the stability and firmness of the protein-ligand complexes throughout the 100ns molecular dynamics simulation. Moreover, the top three compounds exhibited better binding energy along with better stability and firmness than the inhibitor (Nafamostat), which was further confirmed by the binding free energy calculation. Therefore, this computational investigation could aid in the development of efficient therapeutics for life-threatening MERS-CoV infections.
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Affiliation(s)
- Suvro Biswas
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md. Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | | | - Shahriar Zaman
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
| | - Md. Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, 6205, Bangladesh
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16
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Dayan Elshan NGR, Wolff KC, Riva L, Woods AK, Grabovyi G, Wilson K, Pedroarena J, Ghorai S, Nazarian A, Weiss F, Liu Y, Mazumdar W, Song L, Okwor N, Malvin J, Bakowski MA, Beutler N, Kirkpatrick MG, Gebara-Lamb A, Huang E, Nguyen-Tran VTB, Chi V, Li S, Rogers TF, McNamara CW, Gupta AK, Rahimi A, Chen JJ, Joseph SB, Schultz PG, Chatterjee AK. Discovery of CMX990: A Potent SARS-CoV-2 3CL Protease Inhibitor Bearing a Novel Warhead. J Med Chem 2024; 67:2369-2378. [PMID: 38335279 PMCID: PMC10895651 DOI: 10.1021/acs.jmedchem.3c01938] [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: 10/17/2023] [Revised: 11/26/2023] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
There remains a need to develop novel SARS-CoV-2 therapeutic options that improve upon existing therapies by an increased robustness of response, fewer safety liabilities, and global-ready accessibility. Functionally critical viral main protease (Mpro, 3CLpro) of SARS-CoV-2 is an attractive target due to its homology within the coronaviral family, and lack thereof toward human proteases. In this disclosure, we outline the advent of a novel SARS-CoV-2 3CLpro inhibitor, CMX990, bearing an unprecedented trifluoromethoxymethyl ketone warhead. Compared with the marketed drug nirmatrelvir (combination with ritonavir = Paxlovid), CMX990 has distinctly differentiated potency (∼5× more potent in primary cells) and human in vitro clearance (>4× better microsomal clearance and >10× better hepatocyte clearance), with good in vitro-to-in vivo correlation. Based on its compelling preclinical profile and projected once or twice a day dosing supporting unboosted oral therapy in humans, CMX990 advanced to a Phase 1 clinical trial as an oral drug candidate for SARS-CoV-2.
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Affiliation(s)
- N. G. R. Dayan Elshan
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Karen C. Wolff
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Laura Riva
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ashley K. Woods
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gennadii Grabovyi
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Katy Wilson
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - James Pedroarena
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sourav Ghorai
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Armen Nazarian
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Frank Weiss
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yuyin Liu
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Wrickban Mazumdar
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lirui Song
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Neechi Okwor
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jacqueline Malvin
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Malina A. Bakowski
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Nathan Beutler
- Department
of Immunology and Microbiology, The Scripps
Research Institute, 10466
North Torrey Pines Road, La Jolla, California 92037, United States
| | - Melanie G. Kirkpatrick
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Amal Gebara-Lamb
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Edward Huang
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Vân T. B. Nguyen-Tran
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Victor Chi
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Shuangwei Li
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Thomas F. Rogers
- Department
of Immunology and Microbiology, The Scripps
Research Institute, 10466
North Torrey Pines Road, La Jolla, California 92037, United States
| | - Case W. McNamara
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Anil Kumar Gupta
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Alireza Rahimi
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jian Jeffrey Chen
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sean B. Joseph
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Peter G. Schultz
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Arnab K. Chatterjee
- Calibr
at Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, California 92037, United States
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17
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Cyril AC, Ali NM, Nelliyulla Parambath A, Vazhappilly CG, Jan RK, Karuvantevida N, Aburamadan H, Lozon Y, Radhakrishnan R. Nigella sativa and its chemical constituents: pre-clinical and clinical evidence for their potential anti-SARS-CoV-2 effects. Inflammopharmacology 2024; 32:273-285. [PMID: 37966624 DOI: 10.1007/s10787-023-01385-9] [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: 05/01/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused over 500 million reported cases of COVID-19 worldwide with relatively high morbidity and mortality. Although global vaccination drive has helped control the pandemic, the newer variant of the virus still holds the world in ransom. Several medicinal herbs with antiviral properties have been reported, and one such promising herb is Nigella sativa (NS). Recent molecular docking, pre-clinical, and clinical studies have shown that NS extracts may have the potential to prevent the entry of coronaviruses into the host cell as well as to treat and manage COVID-19 symptoms. Several active compounds from NS, such as nigelledine, α-hederin, dithymoquinone (DTQ), and thymoquinone (TQ), have been proposed as excellent ligands to target angiotensin-converting enzyme 2 (ACE2 receptors) and other targets on host cells as well as the spike protein (S protein) on SARS-CoV-2. By binding to these target proteins, these ligands could potentially prevent the binding between ACE2 and S protein. Though several articles have been published on the promising therapeutic role of NS and its constituents against SARS-CoV-2 infection, in this review, we consolidate the published information on NS and SARS-CoV-2, focusing on pre-clinical in silico studies as well as clinical trials reported between 2012 and 2023.
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Affiliation(s)
- Asha Caroline Cyril
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.
| | - Najma Mohamed Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Anagha Nelliyulla Parambath
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Cijo George Vazhappilly
- Department of Biotechnology, American University of Ras Al Khaimah, Ras Al Khaimah, United Arab Emirates
| | - Reem Kais Jan
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Haneen Aburamadan
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Yosra Lozon
- Dubai Pharmacy College for Girls, Dubai, United Arab Emirates
| | - Rajan Radhakrishnan
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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18
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Kralj S, Jukič M, Bahun M, Kranjc L, Kolarič A, Hodošček M, Ulrih NP, Bren U. Identification of Triazolopyrimidinyl Scaffold SARS-CoV-2 Papain-Like Protease (PL pro) Inhibitor. Pharmaceutics 2024; 16:169. [PMID: 38399230 PMCID: PMC10893172 DOI: 10.3390/pharmaceutics16020169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
The global impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its companion disease, COVID-19, has reminded us of the importance of basic coronaviral research. In this study, a comprehensive approach using molecular docking, in vitro assays, and molecular dynamics simulations was applied to identify potential inhibitors for SARS-CoV-2 papain-like protease (PLpro), a key and underexplored viral enzyme target. A focused protease inhibitor library was initially created and molecular docking was performed using CmDock software (v0.2.0), resulting in the selection of hit compounds for in vitro testing on the isolated enzyme. Among them, compound 372 exhibited promising inhibitory properties against PLpro, with an IC50 value of 82 ± 34 μM. The compound also displayed a new triazolopyrimidinyl scaffold not yet represented within protease inhibitors. Molecular dynamics simulations demonstrated the favorable binding properties of compound 372. Structural analysis highlighted its key interactions with PLpro, and we stress its potential for further optimization. Moreover, besides compound 372 as a candidate for PLpro inhibitor development, this study elaborates on the PLpro binding site dynamics and provides a valuable contribution for further efforts in pan-coronaviral PLpro inhibitor development.
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Affiliation(s)
- Sebastjan Kralj
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia
| | - Marko Jukič
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška Ulica 8, SI-6000 Koper, Slovenia
- Institute of Enviormental Protection and Sensors, Beloruska Ulica 7, SI-2000 Maribor, Slovenia
| | - Miha Bahun
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Luka Kranjc
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
- National Institute of Biology, Večna Pot 111, SI-1000 Ljubljana, Slovenia
| | - Anja Kolarič
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia
| | - Milan Hodošček
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Nataša Poklar Ulrih
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Urban Bren
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška Ulica 8, SI-6000 Koper, Slovenia
- Institute of Enviormental Protection and Sensors, Beloruska Ulica 7, SI-2000 Maribor, Slovenia
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19
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Janin YL. On the origins of SARS-CoV-2 main protease inhibitors. RSC Med Chem 2024; 15:81-118. [PMID: 38283212 PMCID: PMC10809347 DOI: 10.1039/d3md00493g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/13/2023] [Indexed: 01/30/2024] Open
Abstract
In order to address the world-wide health challenge caused by the COVID-19 pandemic, the 3CL protease/SARS-CoV-2 main protease (SARS-CoV-2-Mpro) coded by its nsp5 gene became one of the biochemical targets for the design of antiviral drugs. In less than 3 years of research, 4 inhibitors of SARS-CoV-2-Mpro have actually been authorized for COVID-19 treatment (nirmatrelvir, ensitrelvir, leritrelvir and simnotrelvir) and more such as EDP-235, FB-2001 and STI-1558/Olgotrelvir or five undisclosed compounds (CDI-988, ASC11, ALG-097558, QLS1128 and H-10517) are undergoing clinical trials. This review is an attempt to picture this quite unprecedented medicinal chemistry feat and provide insights on how these cysteine protease inhibitors were discovered. Since many series of covalent SARS-CoV-2-Mpro inhibitors owe some of their origins to previous work on other proteases, we first provided a description of various inhibitors of cysteine-bearing human caspase-1 or cathepsin K, as well as inhibitors of serine proteases such as human dipeptidyl peptidase-4 or the hepatitis C protein complex NS3/4A. This is then followed by a description of the results of the approaches adopted (repurposing, structure-based and high throughput screening) to discover coronavirus main protease inhibitors.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université 75005 Paris France
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20
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Wang L, Ding Z, Wang Z, Zhao Y, Wu H, Wei Q, Gao L, Han J. The Development of an Oral Solution Containing Nirmatrelvir and Ritonavir and Assessment of Its Pharmacokinetics and Stability. Pharmaceutics 2024; 16:109. [PMID: 38258119 PMCID: PMC10818454 DOI: 10.3390/pharmaceutics16010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/27/2023] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Paxlovid®, a co-packaged medication comprised of separate tablets containing two active ingredients, nirmatrelvir (NRV) and ritonavir (RTV), exhibits good effectiveness against coronavirus disease 2019 (COVID-19). However, the size of the NRV/RTV tablets makes them difficult for some patients to swallow, especially the elderly and those with dysphagia. Therefore, an oral liquid formulation that can overcome this shortcoming and improve patient compliance is required. In this study, we developed a liquid formulation containing NRV and RTV by adopting strategies that used co-solvents and surfactants to enhance the solubility and inhibit possible recrystallization. The in vitro release results showed that NRV and RTV could be maintained at high concentrations in solution for a certain period in the investigated media. In vivo studies in rats showed that the oral bioavailability of NRV/RTV solution was significantly enhanced. Compared to Paxlovid® tablets, the AUC(0-t) of NRV and RTV increased by 6.1 and 3.8 times, respectively, while the Cmax increased by 5.5 times for both. Furthermore, the promoting effect of the absorption of RTV on the bioavailability of NRV was confirmed. Experiments with a beagle showed a similar trend. Stability studies were also conducted at 4 °C, 25 °C, and 40 °C for 90 days, indicating that the oral liquid formulation was physically and chemically stable. This study can be used as a valuable resource for developing and applying oral liquid NRV/RTV formulations in a clinical context.
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Affiliation(s)
- Lili Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng 252000, China
| | - Zhuang Ding
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng 252000, China
| | - Zhengping Wang
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng 252000, China
| | - Yanna Zhao
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng 252000, China
| | - Hengqian Wu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng 252000, China
| | - Qipeng Wei
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng 252000, China
| | - Lingfeng Gao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Jun Han
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng 252000, China
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21
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Zhang H, Zhou J, Chen H, Mao J, Tang Y, Yan W, Zhang T, Li C, Chen S, Li G, Zhang G, Ding Y, Liu L. Phase I study, and dosing regimen selection for a pivotal COVID-19 trial of GST-HG171. Antimicrob Agents Chemother 2024; 68:e0111523. [PMID: 38099673 PMCID: PMC10777829 DOI: 10.1128/aac.01115-23] [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: 08/28/2023] [Accepted: 10/28/2023] [Indexed: 01/11/2024] Open
Abstract
This study is aimed to evaluate the safety, tolerability, and pharmacokinetics (PK), as well as to select an appropriate dosing regimen for the pivotal clinical trial of GST-HG171, an orally bioavailable, potent, and selective 3CL protease inhibitor by a randomized, double-blind, and placebo-controlled phase I trial in healthy subjects. We conducted a Ph1 study involving 78 healthy subjects to assess the safety, tolerability, and PK of single ascending doses (150-900 mg) as well as multiple ascending doses (MADs) (150 and 300 mg) of GST-HG171. Additionally, we examined the food effect and drug-drug interaction of GST-HG171 in combination with ritonavir through a MAD regimen of GST-HG171/ritonavir (BID or TID) for 5 days. Throughout the course of these studies, no serious AEs or deaths occurred, and no AEs necessitated study discontinuation. We observed that food had no significant impact on the exposure of GST-HG171. However, the presence of ritonavir substantially increased the exposure of GST-HG171, which facilitated the selection of the GST-HG171/ritonavir dose and regimen (150/100 mg BID) for subsequent phase II/III trials. The selected dose regimen was achieved through concentrations continuously at 6.2-9.9-fold above the levels required for protein-binding adjusted 50% inhibition (IC50) of viral replication in vitro. The combination of 150 mg GST-HG171/100 mg ritonavir demonstrated favorable safety and tolerability profiles. The PK data obtained from GST-HG171/ritonavir administration guided the selection of appropriate dose for a pivotal phase II/III trial currently in progress. (This study has been registered at ClinicalTrials.gov under identifier NCT05668897).
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Affiliation(s)
- Hong Zhang
- 1 Phase I Clinical Research Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Jing Zhou
- 1 Phase I Clinical Research Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Hong Chen
- 1 Phase I Clinical Research Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - John Mao
- Fujian Akeylink Biotechnology Co., Ltd., Fuzhou, Fujian, China
| | - Yanan Tang
- Fujian Akeylink Biotechnology Co., Ltd., Fuzhou, Fujian, China
| | - Wenhao Yan
- Fujian Akeylink Biotechnology Co., Ltd., Fuzhou, Fujian, China
| | - Tianxiang Zhang
- Fujian Akeylink Biotechnology Co., Ltd., Fuzhou, Fujian, China
| | - Chuanjing Li
- Fujian Akeylink Biotechnology Co., Ltd., Fuzhou, Fujian, China
| | - Shikui Chen
- Fujian Cosunter Pharmaceutical Co., Ltd., Fuzhou, Fujian, China
| | - Guoping Li
- Fujian Cosunter Pharmaceutical Co., Ltd., Fuzhou, Fujian, China
| | - George Zhang
- Fujian Akeylink Biotechnology Co., Ltd., Fuzhou, Fujian, China
| | - Yanhua Ding
- 1 Phase I Clinical Research Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Li Liu
- Department of Pediatrics, The First Hospital of Jilin University, Changchun, Jilin, China
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22
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Zargari F, Mohammadi M, Nowroozi A, Morowvat MH, Nakhaei E, Rezagholi F. The Inhibitory Effects of the Herbals Secondary Metabolites (7α-acetoxyroyleanone, Curzerene, Incensole, Harmaline, and Cannabidiol) on COVID-19: A Molecular Docking Study. Recent Pat Biotechnol 2024; 18:316-331. [PMID: 38817009 DOI: 10.2174/0118722083246773231108045238] [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: 04/04/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 06/01/2024]
Abstract
BACKGROUND Since the COVID-19 outbreak in early 2020, researchers and studies are continuing to find drugs and/or vaccines against the disease. As shown before, medicinal plants can be very good sources against viruses because of their secondary compounds which may cure diseases and help in survival of patients. There is a growing trend in the filed patents in this field. AIMS In the present study, we test and suggest the inhibitory potential of five herbal based extracts including 7α-acetoxyroyleanone, Curzerene, Incensole, Harmaline, and Cannabidiol with antivirus activity on the models of the significant antiviral targets for COVID-19 like spike glycoprotein, Papain-like protease (PLpro), non-structural protein 15 (NSP15), RNA-dependent RNA polymerase and core protease by molecular docking study. METHODS The Salvia rythida root was extracted, dried, and pulverized by a milling machine. The aqueous phase and the dichloromethane phase of the root extractive were separated by two-phase extraction using a separatory funnel. The separation was performed using the column chromatography method. The model of the important antivirus drug target of COVID-19 was obtained from the Protein Data Bank (PDB) and modified. TO study the binding difference between the studied molecules, the docking study was performed. RESULTS These herbal compounds are extracted from Salvia rhytidea, Curcuma zeodaria, Frankincense, Peganum harmala, and Cannabis herbs, respectively. The binding energies of all compounds on COVID-19 main targets are located in the limited area of 2.22-5.30 kcal/mol. This range of binding energies can support our hypothesis for the presence of the inhibitory effects of the secondary metabolites of mentioned structures on COVID-19. Generally, among the investigated herbal structures, Cannabidiol and 7α- acetoxyroyleanone compounds with the highest binding energy have the most inhibitory potential. The least inhibitory effects are related to the Curzerene and Incensole structures by the lowest binding affinity. CONCLUSION The general arrangement of the basis of the potential barrier of binding energies is in the order below: Cannabidiol > 7α-acetoxyroyleanone > Harmaline> Incensole > Curzerene. Finally, the range of docking scores for investigated herbal compounds on the mentioned targets indicates that the probably inhibitory effects on these targets obey the following order: main protease> RNA-dependent RNA polymerase> PLpro> NSP15> spike glycoprotein.
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Affiliation(s)
- Farshid Zargari
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan (USB), P.O.Box 98135- 674, Zahedan, Iran
| | - Mehdi Mohammadi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Box 71468-64685, Shiraz, Iran
| | - Alireza Nowroozi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan (USB), P.O.Box 98135- 674, Zahedan, Iran
| | - Mohammad Hossein Morowvat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Box 71468-64685, Shiraz, Iran
| | - Ebrahim Nakhaei
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan (USB), P.O.Box 98135- 674, Zahedan, Iran
| | - Fatemeh Rezagholi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Box 71468-64685, Shiraz, Iran
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23
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Song L, Gao S, Ye B, Yang M, Cheng Y, Kang D, Yi F, Sun JP, Menéndez-Arias L, Neyts J, Liu X, Zhan P. Medicinal chemistry strategies towards the development of non-covalent SARS-CoV-2 M pro inhibitors. Acta Pharm Sin B 2024; 14:87-109. [PMID: 38239241 PMCID: PMC10792984 DOI: 10.1016/j.apsb.2023.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/10/2023] [Accepted: 08/02/2023] [Indexed: 01/22/2024] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is an attractive target in anti-COVID-19 therapy for its high conservation and major role in the virus life cycle. The covalent Mpro inhibitor nirmatrelvir (in combination with ritonavir, a pharmacokinetic enhancer) and the non-covalent inhibitor ensitrelvir have shown efficacy in clinical trials and have been approved for therapeutic use. Effective antiviral drugs are needed to fight the pandemic, while non-covalent Mpro inhibitors could be promising alternatives due to their high selectivity and favorable druggability. Numerous non-covalent Mpro inhibitors with desirable properties have been developed based on available crystal structures of Mpro. In this article, we describe medicinal chemistry strategies applied for the discovery and optimization of non-covalent Mpro inhibitors, followed by a general overview and critical analysis of the available information. Prospective viewpoints and insights into current strategies for the development of non-covalent Mpro inhibitors are also discussed.
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Affiliation(s)
- Letian Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, China
| | - Bing Ye
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Mianling Yang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yusen Cheng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Fan Yi
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan 250012, China
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Científicas & Autonomous University of Madrid), Madrid 28049, Spain
| | - Johan Neyts
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven 3000, Belgium
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
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24
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Rocho FR, Snipas SJ, Shamim A, Rut W, Drag M, Montanari CA, Salvesen GS. Differential specificity of SARS-CoV-2 main protease variants on peptide versus protein-based substrates. FEBS J 2024; 291:61-69. [PMID: 37843490 DOI: 10.1111/febs.16970] [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: 05/27/2023] [Revised: 08/17/2023] [Accepted: 10/05/2023] [Indexed: 10/17/2023]
Abstract
The SARS-CoV-2 main protease (Mpro ) holds significant importance as a biological target in combating coronaviruses due to its importance in virus replication. Considering the emergence of novel SARS-CoV-2 variants and the mutations observed in the Mpro sequence, we hypothesized that these mutations may have a potential impact on the protease's specificity. To test this, we expressed Mpro corresponding to the original strain and variants Beta1, Beta2, and Omicron and analyzed their activity on protein-based and peptide substrates. Although we observed differential activity on the protein-based substrate, there was very little difference when analyzed on the peptide substrate. We conclude that mutations on the Mpro sequence, despite having a minor effect on a peptide substrate cleavage, did not change the catalytic site environment enough to build resistance to inhibition. Therefore, we propose that inhibitors initially designed for the Mpro of the original strain will be effective in all the variants. Thus, Mpro is likely to continue to be a target of therapeutic interest as mutations in its sequence are rare and, as we show here, have a minor effect on the protease's recognition of peptide-based molecules.
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Affiliation(s)
- Fernanda R Rocho
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Medicinal and Biological Chemistry Group of the Department of Chemistry and Molecular Physics, University of São Paulo, Brazil
| | - Scott J Snipas
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Anwar Shamim
- Medicinal and Biological Chemistry Group of the Department of Chemistry and Molecular Physics, University of São Paulo, Brazil
| | - Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Poland
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Poland
| | - Carlos A Montanari
- Medicinal and Biological Chemistry Group of the Department of Chemistry and Molecular Physics, University of São Paulo, Brazil
| | - Guy S Salvesen
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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Mia ME, Howlader M, Akter F, Hossain MM. Preclinical and Clinical Investigations of Potential Drugs and Vaccines for COVID-19 Therapy: A Comprehensive Review With Recent Update. CLINICAL PATHOLOGY (THOUSAND OAKS, VENTURA COUNTY, CALIF.) 2024; 17:2632010X241263054. [PMID: 39070952 PMCID: PMC11282570 DOI: 10.1177/2632010x241263054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 06/03/2024] [Indexed: 07/30/2024]
Abstract
The COVID-19 pandemic-led worldwide healthcare crisis necessitates prompt societal, ecological, and medical efforts to stop or reduce the rising number of fatalities. Numerous mRNA based vaccines and vaccines for viral vectors have been licensed for use in emergencies which showed 90% to 95% efficacy in preventing SARS-CoV-2 infection. However, safety issues, vaccine reluctance, and skepticism remain major concerns for making mass vaccination a successful approach to treat COVID-19. Hence, alternative therapeutics is needed for eradicating the global burden of COVID-19 from developed and low-resource countries. Repurposing current medications and drug candidates could be a more viable option for treating SARS-CoV-2 as these therapies have previously passed a number of significant checkpoints for drug development and patient care. Besides vaccines, this review focused on the potential usage of alternative therapeutic agents including antiviral, antiparasitic, and antibacterial drugs, protease inhibitors, neuraminidase inhibitors, and monoclonal antibodies that are currently undergoing preclinical and clinical investigations to assess their effectiveness and safety in the treatment of COVID-19. Among the repurposed drugs, remdesivir is considered as the most promising agent, while favipiravir, molnupiravir, paxlovid, and lopinavir/ritonavir exhibited improved therapeutic effects in terms of elimination of viruses. However, the outcomes of treatment with oseltamivir, umifenovir, disulfiram, teicoplanin, and ivermectin were not significant. It is noteworthy that combining multiple drugs as therapy showcases impressive effectiveness in managing individuals with COVID-19. Tocilizumab is presently employed for the treatment of patients who exhibit COVID-19-related pneumonia. Numerous antiviral drugs such as galidesivir, griffithsin, and thapsigargin are under clinical trials which could be promising for treating COVID-19 individuals with severe symptoms. Supportive treatment for patients of COVID-19 may involve the use of corticosteroids, convalescent plasma, stem cells, pooled antibodies, vitamins, and natural substances. This study provides an updated progress in SARS-CoV-2 medications and a crucial guide for inventing novel interventions against COVID-19.
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Affiliation(s)
- Md. Easin Mia
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Mithu Howlader
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Farzana Akter
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md. Murad Hossain
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
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Alagarsamy V, Solomon VR, Murugesan S, Sundar PS, Muzaffar-Ur-Rehman MD, Chandu A, Aishwarya AD, Narendhar B, Sulthana MT, Ravikumar V. In Silico Screening of Some Active Phytochemicals to Identify Promising Inhibitors Against SARS-CoV-2 Targets. Curr Drug Discov Technol 2024; 21:73-89. [PMID: 37861016 DOI: 10.2174/0115701638243222230920051050] [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: 01/19/2023] [Revised: 07/29/2023] [Accepted: 08/09/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND There are very few small-molecule drug candidates developed against SARS-CoV-2 that have been revealed since the epidemic began in November 2019. The typical medicinal chemistry discovery approach requires more than a decade of the year of painstaking research and development and a significant financial guarantee, which is not feasible in the challenge of the current epidemic. OBJECTIVE This current study proposes to find and identify the most effective and promising phytomolecules against SARS-CoV-2 in six essential proteins (3CL protease, Main protease, Papain- Like protease, N-protein RNA binding domain, RNA-dependent RNA polymerase, and Spike receptor binding domain target through in silico screening of 63 phytomolecules from six different Ayurveda medicinal plants. METHODS The phytomolecules and SARS-CoV-2 proteins were taken from public domain databases such as PubChem and RCSB Protein Data Bank. For in silico screening, the molecular interactions, binding energy, and ADMET properties were investigated. RESULTS The structure-based molecular docking reveals some molecules' greater affinity towards the target than the co-crystal ligand. Our results show that tannic acid, cyanidin-3-rutinoside, zeaxanthin, and carbolactone are phytomolecules capable of inhibiting SARS-CoV-2 target proteins in the least energy conformations. Tannic acid had the least binding energy of -8.8 kcal/mol, which is better than the binding energy of its corresponding co-crystal ligand (-7.5 kcal/mol) against 3 CL protease. Also, it has shown the least binding energy of -9.9 kcal/mol with a more significant number of conventional hydrogen bond interactions against the RdRp target. Cyanidin-3-rutinoside showed binding energy values of -8.8 and -7.6 kcal/mol against Main protease and Papain-like protease, respectively. Zeaxanthin was the top candidate in the N protein RBD with a binding score of - 8.4 kcal/mol, which is slightly better when compared to a co-crystal ligand (-8.2 kcal/mol). In the spike, carbolactone was the suitable candidate with the binding energy of -7.2 kcal/mol and formed a conventional hydrogen bond and two hydrophobic interactions. The best binding affinity-scored phytomolecules were selected for the MD simulations studies. CONCLUSION The present in silico screening study suggested that active phytomolecules from medicinal plants could inhibit SARS-CoV-2 targets. The elite docked compounds with drug-like properties have a harmless ADMET profile, which may help to develop promising COVID-19 inhibitors.
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Affiliation(s)
- V Alagarsamy
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Gr. Hyderabad, 502 294, India
| | - V Raja Solomon
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Gr. Hyderabad, 502 294, India
| | - S Murugesan
- Department of Pharmacy, BITS Pilani, Pilani Campus, Pilani, 333031, India
| | - P Shyam Sundar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Gr. Hyderabad, 502 294, India
| | | | - A Chandu
- Department of Pharmacy, BITS Pilani, Pilani Campus, Pilani, 333031, India
| | - A Dharshini Aishwarya
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Gr. Hyderabad, 502 294, India
| | - B Narendhar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Gr. Hyderabad, 502 294, India
| | - M T Sulthana
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Gr. Hyderabad, 502 294, India
| | - V Ravikumar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy - 502 294, Gr. Hyderabad, India
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Trivedi A, Kardam V, Inampudi KK, Vrati S, Gupta D, Singh A, Kayampeta SR, Appaiahgari MB, Sehgal D. Identification of a novel inhibitor of SARS-CoV-2 main protease: an in silico, biochemical, and cell-based approach. FEBS J 2023; 290:5496-5513. [PMID: 37657928 DOI: 10.1111/febs.16947] [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: 05/25/2023] [Revised: 07/06/2023] [Accepted: 08/31/2023] [Indexed: 09/03/2023]
Abstract
The recurrent nature of coronavirus outbreaks, severity of the COVID-19 pandemic, rapid emergence of novel variants, and concerns over the effectiveness of existing vaccines against novel variants have highlighted the need to develop therapeutic interventions. Targeted efforts to identify inhibitors of crucial viral proteins are the preferred strategy. In this study, we screened FDA-approved and natural product libraries using in silico approach for potential hits against the SARS-CoV-2 main protease (Mpro) and experimentally validated their potency using in vitro biochemical and cell-based assays. Seven potential hits were identified through in silico screening and were subsequently evaluated in SARS-CoV-2-based cell-free assays, followed by testing in the HCoV-229E-based culture system. Of the tested compounds, 4-(3,4-dihydroxyphenyl)-6,7-dihydroxy-1-isopropyl-1H-benzofuro[3,2-b]pyrazolo[4,3-e]pyridin-3(2H)-one (PubChem CID:71755304, hereafter referred to as STL522228) exhibited significant antiviral activity. Subsequently, its potential as a novel COVID therapeutic molecule was validated in the SARS-CoV-2-culture system, where STL522228 demonstrated superior antiviral activity (EC50 = 0.44 μm) compared to Remdesivir (EC50 = 0.62 μm). Based on these findings, we report the strong anti-coronavirus activity of STL522228, and propose that it as a promising pan-coronavirus Mpro inhibitor for further experimental and preclinical validation.
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Affiliation(s)
- Aditya Trivedi
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
| | - Vandana Kardam
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
| | | | - Sudhanshu Vrati
- Laboratory of Virology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Dharmender Gupta
- Laboratory of Virology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Aekagra Singh
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
| | - Sarala Rani Kayampeta
- Research and Development Division, Srikara Biologicals Private Limited, Tirupati, India
| | | | - Deepak Sehgal
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
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Botha S, Fromme P. Review of serial femtosecond crystallography including the COVID-19 pandemic impact and future outlook. Structure 2023; 31:1306-1319. [PMID: 37898125 PMCID: PMC10842180 DOI: 10.1016/j.str.2023.10.005] [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: 07/18/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/30/2023]
Abstract
Serial femtosecond crystallography (SFX) revolutionized macromolecular crystallography over the past decade by enabling the collection of X-ray diffraction data from nano- or micrometer sized crystals while outrunning structure-altering radiation damage effects at room temperature. The serial manner of data collection from millions of individual crystals coupled with the femtosecond duration of the ultrabright X-ray pulses enables time-resolved studies of macromolecules under near-physiological conditions to unprecedented temporal resolution. In 2020 the rapid spread of the coronavirus SARS-CoV-2 resulted in a global pandemic of coronavirus disease-2019. This led to a shift in how serial femtosecond experiments were performed, along with rapid funding and free electron laser beamtime availability dedicated to SARS-CoV-2-related studies. This review outlines the current state of SFX research, the milestones that were achieved, the impact of the global pandemic on this field as well as an outlook into exciting future directions.
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Affiliation(s)
- Sabine Botha
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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Yu Z, Zheng Y, Chen B, Lv J, Zhu X, Shang B, Xv Y, Tao R, Yang Y, Cong J, Li D, Wu H, Qv W, Zhang X, Xv C, Feng H, Yuan W, Gao Y. Efficacy and safety of Huashi Baidu granule plus Nirmatrelvir-Ritonavir combination therapy in patients with high-risk factors infected with Omicron (B.1.1.529): A multi-arm single-center, open-label, randomized controlled trial. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 120:155025. [PMID: 37639813 DOI: 10.1016/j.phymed.2023.155025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/31/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND Huashi Baidu granule (HSBD) and Paxlovid (Nirmatrelvir-Ritonavir) are antiviral Chinese patent medicine and western medicine specially developed for treating coronavirus disease 2019 (COVID-19). Their efficacy and safety in treating COVID-19 are still under investigated. PURPOSE To assess and compare the efficacy and safety of HSBD, Paxlovid, and the combination in treating high-risk patients infected with SARS-CoV-2 Omicron. STUDY DESIGN The study was a prospective single-center, open-label, randomized, controlled clinical trial conducted from April 18 to June 5, 2022. (ClinicalTrial.gov registration number: ChiCTR2200059390) METHODS: 312 severe patients aged 18 years and older infected with SARS-CoV-2 Omicron from Shuguang Hospital in Shanghai were randomly allocated to HSBD monotherapy (orally 137 g twice daily for 7 days, n = 105), Paxlovid monotherapy (orally 300 mg of Nirmatrelvir plus 100 mg of Ritonavir every 12 h for 5 days, n = 103), or combination therapy (n = 104). The primary outcome was SARS-CoV-2 nucleic acid negative conversion within 7-day treatment. The secondary outcome included hospital discharging conditions, severe conversion of symptom, and adverse events. RESULTS Of 312 participants, 85 (82%) of 104 in combination therapy, 71 (68%) of 105 in HSBD monotherapy, and 73 (71%) of 103 in Paxlovid monotherapy had a primary outcome event. The hazard ratios of primary outcome were 1.37 (95% CI 1.03 - 1.84, p = 0.012) for combination versus HSBD, 1.28 (0.98-1.69, p = 0.043) for combination versus Paxlovid, and 0.88 (0.66-1.18, p = 0.33) for HSBD versus Paxlovid. There was no statistical difference of efficacy between HSBD and Paxlovid, while combination therapy exhibited more effective than either alone. For secondary outcomes, the hospital discharging rates within 7 days exhibited the significant increase in combination therapy than in HSBD or Paxlovid monotherapy (71% (74/104) vs 55% (58/105) vs 52% (54/103), p < 0.05). The risk of severe conversion of symptom showed no statistical significance among three interventions (1% (1/104) vs 3% (3/105) vs 3% (3/103), p > 0.05). No severe adverse events occurred among combination therapy and monotherapies in the trial. CONCLUSION For patients with severe COVID-19, HSBD exhibits similar efficacy to Paxlovid, while combination therapy is more likely to increase the curative efficacy of Omicron variant than monotherapies, with few serious adverse events.
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Affiliation(s)
- Zhuo Yu
- Department of Hepatopathy, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Team of COVID-19 Epidemic Prevention and Treatment, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yanxi Zheng
- Department of Hepatopathy, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Team of COVID-19 Epidemic Prevention and Treatment, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Bowu Chen
- Department of Hepatopathy, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Team of COVID-19 Epidemic Prevention and Treatment, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jia Lv
- Department of Hepatopathy, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Team of COVID-19 Epidemic Prevention and Treatment, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xiaojun Zhu
- Department of Hepatopathy, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Team of COVID-19 Epidemic Prevention and Treatment, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Binyi Shang
- Department of Hepatopathy, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Team of COVID-19 Epidemic Prevention and Treatment, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yuping Xv
- Nursing Department, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ru Tao
- Nursing Department, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yanbing Yang
- Nursing Department, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jun Cong
- Team of COVID-19 Epidemic Prevention and Treatment, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Dan Li
- Team of COVID-19 Epidemic Prevention and Treatment, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Huan Wu
- Team of COVID-19 Epidemic Prevention and Treatment, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Wenchao Qv
- Team of COVID-19 Epidemic Prevention and Treatment, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xiyi Zhang
- Department of Informatics, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Chengbin Xv
- Department of Informatics, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hai Feng
- Institute of Infectious Disease, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Weian Yuan
- Centre of Good Clinical Practice, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yueqiu Gao
- Department of Hepatopathy, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Institute of Infectious Disease, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Team of COVID-19 Epidemic Prevention and Treatment, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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30
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Chen X, Leyendecker S, van den Bedem H. SARS-CoV-2 main protease mutation analysis via a kinematic method. Proteins 2023; 91:1496-1509. [PMID: 37408369 DOI: 10.1002/prot.26543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 05/23/2023] [Accepted: 06/08/2023] [Indexed: 07/07/2023]
Abstract
The Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is the virus responsible for the COVID-19 pandemic. COVID-19 continues to cause millions of deaths globally in part due to immune-evading mutations. SARS-CoV-2 main protease (Mpro) is an important enzyme for viral replication and potentially an effective drug target. Mutations affect the dynamics of enzymes and thereby their activity and ability to bind ligands. Here, we use kinematic flexibility analysis (KFA) to identify how mutations and ligand binding changes the conformational flexibility of Mpro. KFA decomposes macromolecules into regions of different flexibility near-instantly from a static structure, allowing conformational dynamics analysis at scale. Altogether, we analyzed 47 mutation sites across 69 Mpro-ligand complexes resulting in more than 3300 different structures which includes 69 mutated structures with all 47 sites mutated simultaneously and 3243 single residue mutated structures. We found that mutations generally increased the conformational flexibility of the protein. Understanding the impact of mutations on the flexibility of Mpro is essential for identifying potential drug targets in the treatment of SARS-CoV-2. Further studies in this area can offer valuable insights into the mechanisms of molecular recognition.
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Affiliation(s)
- Xiyu Chen
- Department of Mechanical Engineering, Institute of Applied Dynamics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sigrid Leyendecker
- Department of Mechanical Engineering, Institute of Applied Dynamics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Henry van den Bedem
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
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Jiang X, Su H, Shang W, Zhou F, Zhang Y, Zhao W, Zhang Q, Xie H, Jiang L, Nie T, Yang F, Xiong M, Huang X, Li M, Chen P, Peng S, Xiao G, Jiang H, Tang R, Zhang L, Shen J, Xu Y. Structure-based development and preclinical evaluation of the SARS-CoV-2 3C-like protease inhibitor simnotrelvir. Nat Commun 2023; 14:6463. [PMID: 37833261 PMCID: PMC10575921 DOI: 10.1038/s41467-023-42102-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The persistent pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants accentuates the great demand for developing effective therapeutic agents. Here, we report the development of an orally bioavailable SARS-CoV-2 3C-like protease (3CLpro) inhibitor, namely simnotrelvir, and its preclinical evaluation, which lay the foundation for clinical trials studies as well as the conditional approval of simnotrelvir in combination with ritonavir for the treatment of COVID-19. The structure-based optimization of boceprevir, an approved HCV protease inhibitor, leads to identification of simnotrelvir that covalently inhibits SARS-CoV-2 3CLpro with an enthalpy-driven thermodynamic binding signature. Multiple enzymatic assays reveal that simnotrelvir is a potent pan-CoV 3CLpro inhibitor but has high selectivity. It effectively blocks replications of SARS-CoV-2 variants in cell-based assays and exhibits good pharmacokinetic and safety profiles in male and female rats and monkeys, leading to robust oral efficacy in a male mouse model of SARS-CoV-2 Delta infection in which it not only significantly reduces lung viral loads but also eliminates the virus from brains. The discovery of simnotrelvir thereby highlights the utility of structure-based development of marked protease inhibitors for providing a small molecule therapeutic effectively combatting human coronaviruses.
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Affiliation(s)
- Xiangrui Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Weijuan Shang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, 430071, Wuhan, China
| | - Feng Zhou
- State Key Laboratory of Neurology and Oncology Drug Development, 210023, Nanjing, China
- Simcere Zaiming Pharmaceutical Co., Ltd, 200000, Shanghai, China
| | - Yan Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Wenfeng Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Qiumeng Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Hang Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 210023, Nanjing, China
| | - Lei Jiang
- Simcere Zaiming Pharmaceutical Co., Ltd, 200000, Shanghai, China
| | - Tianqing Nie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 210023, Nanjing, China
| | - Feipu Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Muya Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaoxing Huang
- Simcere Zaiming Pharmaceutical Co., Ltd, 200000, Shanghai, China
| | - Minjun Li
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 201210, Shanghai, China
| | - Ping Chen
- Jiangsu Simcere Pharmaceutical Co., Ltd, 210023, Nanjing, China
| | - Shaoping Peng
- State Key Laboratory of Neurology and Oncology Drug Development, 210023, Nanjing, China
- Jiangsu Simcere Pharmaceutical Co., Ltd, 210023, Nanjing, China
| | - Gengfu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, 430071, Wuhan, China
| | - Hualiang Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Renhong Tang
- State Key Laboratory of Neurology and Oncology Drug Development, 210023, Nanjing, China.
- Simcere Zaiming Pharmaceutical Co., Ltd, 200000, Shanghai, China.
| | - Leike Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, 430071, Wuhan, China.
- Hubei jiangxia Laboratory, 430200, Wuhan, China.
| | - Jingshan Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 310024, Hangzhou, China.
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Tsuji K, Ishii T, Kobayakawa T, Higashi-Kuwata N, Shinohara K, Azuma C, Miura Y, Nakano H, Wada N, Hattori SI, Bulut H, Mitsuya H, Tamamura H. Structure-Activity Relationship Studies of SARS-CoV-2 Main Protease Inhibitors Containing 4-Fluorobenzothiazole-2-carbonyl Moieties. J Med Chem 2023; 66:13516-13529. [PMID: 37756225 DOI: 10.1021/acs.jmedchem.3c00777] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
The main protease (Mpro) of SARS-CoV-2 is an attractive target for the development of drugs to treat COVID-19. Here, we report the design, synthesis, and structure-activity relationship (SAR) studies of highly potent SARS-CoV-2 Mpro inhibitors including TKB245 (5)/TKB248 (6). Since we have previously developed Mpro inhibitors (3) and (4), several hybrid molecules of these previous compounds combined with nirmatrelvir (1) were designed and synthesized. Compounds such as TKB245 (5) and TKB248 (6), containing a 4-fluorobenzothiazole moiety at the P1' site, are highly effective in the blockade of SARS-CoV-2 replication in VeroE6 cells. Replacement of the P1-P2 amide with the thioamide surrogate in TKB248 (6) improved its PK profile in mice compared to that of TKB245 (5). A new diversity-oriented synthetic route to TKB245 (5) derivatives was also developed. The results of the SAR studies suggest that TKB245 (5) and TKB248 (6) are useful lead compounds for the further development of Mpro inhibitors.
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Affiliation(s)
- Kohei Tsuji
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takahiro Ishii
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takuya Kobayakawa
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Nobuyo Higashi-Kuwata
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Kouki Shinohara
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Chika Azuma
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Yutaro Miura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Hiroki Nakano
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Naoya Wada
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
| | - Shin-Ichiro Hattori
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Haydar Bulut
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Hiroaki Mitsuya
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Shinjuku-ku, Tokyo 162-8655, Japan
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
- Department of Clinical Sciences, Kumamoto University Hospital, Chuo-ku, Kumamoto 860-8556, Japan
| | - Hirokazu Tamamura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), Chiyoda-ku, Tokyo 101-0062, Japan
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Duan Y, Wang H, Yuan Z, Yang H. Structural biology of SARS-CoV-2 M pro and drug discovery. Curr Opin Struct Biol 2023; 82:102667. [PMID: 37544112 DOI: 10.1016/j.sbi.2023.102667] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/10/2023] [Accepted: 07/10/2023] [Indexed: 08/08/2023]
Abstract
Since its outbreak in late 2019, the COVID-19 pandemic has drawn enormous attention worldwide as a consequence of being the most disastrous infectious disease in the past century. As one of the most immediately druggable targets of SARS-CoV-2, the main protease (Mpro) has been studied thoroughly. In this review, we provide a comprehensive summary of recent advances in structural studies of Mpro, which provide new knowledge about Mpro in terms of its biological function, structural characteristics, substrate specificity, and autocleavage process. We examine the remarkable strides made in targeting Mpro for drug discovery during the pandemic. We summarize insights into the current understanding of the structural features of Mpro and the discovery of existing Mpro-targeting drugs, illuminating pathways for the future development of anti-SARS-CoV-2 therapeutics.
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Affiliation(s)
- Yinkai Duan
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Haofeng Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences and Institute of Infectious Disease and Biosecurity, Shanghai Medical College of Fudan University, Shanghai, China.
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Shanghai Clinical Research and Trial Center, Shanghai, China.
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Citarella A, Dimasi A, Moi D, Passarella D, Scala A, Piperno A, Micale N. Recent Advances in SARS-CoV-2 Main Protease Inhibitors: From Nirmatrelvir to Future Perspectives. Biomolecules 2023; 13:1339. [PMID: 37759739 PMCID: PMC10647625 DOI: 10.3390/biom13091339] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/28/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
The main protease (Mpro) plays a pivotal role in the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is considered a highly conserved viral target. Disruption of the catalytic activity of Mpro produces a detrimental effect on the course of the infection, making this target one of the most attractive for the treatment of COVID-19. The current success of the SARS-CoV-2 Mpro inhibitor Nirmatrelvir, the first oral drug for the treatment of severe forms of COVID-19, has further focused the attention of researchers on this important viral target, making the search for new Mpro inhibitors a thriving and exciting field for the development of antiviral drugs active against SARS-CoV-2 and related coronaviruses.
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Affiliation(s)
- Andrea Citarella
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy; (A.D.); (D.P.)
| | - Alessandro Dimasi
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy; (A.D.); (D.P.)
| | - Davide Moi
- Department of Chemical and Geological Sciences, University of Cagliari, S.P. 8 CA, 09042 Cagliari, Italy;
| | - Daniele Passarella
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy; (A.D.); (D.P.)
| | - Angela Scala
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy; (A.S.); (A.P.)
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy; (A.S.); (A.P.)
| | - Nicola Micale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy; (A.S.); (A.P.)
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Hans N, Gupta S, Patel AK, Naik S, Malik A. Deciphering the role of fucoidan from brown macroalgae in inhibiting SARS-CoV-2 by targeting its main protease and receptor binding domain: Invitro and insilico approach. Int J Biol Macromol 2023; 248:125950. [PMID: 37487999 DOI: 10.1016/j.ijbiomac.2023.125950] [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: 02/12/2023] [Revised: 07/04/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
The current study investigated the role of fucoidan from Padina tetrastromatica and Turbinaria conoides against 3-chymotrypsin like protease (3CLpro) and receptor binding domain (RBD) spike protein of SARS-CoV-2 using an invitro and computational approach. The 3CLpro and RBD genes were successfully cloned in pET28a vector, expressed in BL-21DE3 E. coli rosetta cells and purified by ion exchange affinity and size exclusion chromatography. Fucoidan extracted from both biomass using green approach, subcritical water, was found to inhibit 3CLpro of SARS-CoV-2 with an IC50 value of up to 0.35 mg mL-1. However, fucoidan was found to be inactive against the RBD protein. Molecular docking studies demonstrated that fucoidan binds to the active sites of 3CLpro with an affinity of -5.0 kcal mol-1. In addition, molecular dynamic simulations recorded stabilized interactions of protein-ligand complexes in terms of root mean square deviation, root mean square fluctuation, the radius of gyration, solvent accessible surface area and hydrogen bond interaction. The binding energy of fucoidan with 3CLpro was determined to be -101.821 ± 12.966 kJ mol-1 using Molecular Mechanic/Poisson-Bolt-Boltzmann Surface Area analysis. Fucoidan satisfies the Absorption, Distribution, Metabolism, and Excretion (ADME) properties, including Lipinski's rule of five, which play an essential role in drug design. According to the toxicity parameters, fucoidan does not exhibit skin sensitivity, hepatotoxicity, or AMES toxicity. Therefore, this work reveals that fucoidan from brown macroalgae could act as possible inhibitors in regulating the function of the 3CLpro protein, hence inhibiting viral replication and being effective against COVID-19.
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Affiliation(s)
- Nidhi Hans
- Supercritical Fluid Extraction Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, New Delhi 110016, India
| | - Shreya Gupta
- Kausma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, Delhi 110016, India
| | - Ashok Kumar Patel
- Kausma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, Delhi 110016, India.
| | - Satyanarayan Naik
- Supercritical Fluid Extraction Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, New Delhi 110016, India.
| | - Anushree Malik
- Applied Microbiology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, New Delhi 110016, India.
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Cox DS, Van Eyck L, Pawlak S, Beckerman B, Linn C, Ginman K, Thay Cha Y, LaBadie RR, Shi H, Damle B. Effects of itraconazole and carbamazepine on the pharmacokinetics of nirmatrelvir/ritonavir in healthy adults. Br J Clin Pharmacol 2023; 89:2867-2876. [PMID: 37184075 DOI: 10.1111/bcp.15788] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/16/2023] Open
Abstract
AIMS The objective of this study was to evaluate the effects of a strong cytochrome P450 family (CYP) 3A4 inhibitor (itraconazole) and inducer (carbamazepine) on the pharmacokinetics and safety of nirmatrelvir/ritonavir. METHODS Pharmacokinetics were measured in two phase 1, open-label, fixed-sequence studies in healthy adults. During Period 1, oral nirmatrelvir/ritonavir 300 mg/100 mg twice daily was administered alone; during Period 2, it was administered with itraconazole or carbamazepine. Nirmatrelvir/ritonavir was administered as repeated doses or one dose in the itraconazole and carbamazepine studies, respectively. Nirmatrelvir and ritonavir plasma concentrations and adverse event (AE) rates in both periods were analysed. RESULTS Each study included 12 participants. Following administration of nirmatrelvir/ritonavir with itraconazole (Test) or alone (Reference), test/reference ratios of the adjusted geometric means (90% CIs) for nirmatrelvir AUCtau and Cmax were 138.82% (129.25%, 149.11%) and 118.57% (112.50%, 124.97%), respectively. After administration of nirmatrelvir/ritonavir with carbamazepine (Test) or alone (Reference), test/reference ratios (90% CIs) of the adjusted geometric means for nirmatrelvir AUCinf and Cmax were 44.50% (33.77%, 58.65%) and 56.82% (47.04%, 68.62%), respectively. Nirmatrelvir/ritonavir was generally safe when administered with or without itraconazole or carbamazepine. No serious or severe AEs were reported. CONCLUSIONS Coadministration of a strong CYP3A4 inhibitor with a strong CYP3A inhibitor used for pharmacokinetic enhancement (i.e., ritonavir) resulted in small increases in plasma nirmatrelvir exposure, whereas coadministration of a strong inducer substantially decreased systemic nirmatrelvir and ritonavir exposures suggesting a contraindication in the label with CYP3A4 strong inducers. Administration of nirmatrelvir/ritonavir alone or with itraconazole or carbamazepine was generally safe.
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Affiliation(s)
- Donna S Cox
- Global Product Development, Pfizer Inc., Collegeville, Pennsylvania, USA
| | - Lien Van Eyck
- Clinical Research Unit, Pfizer Inc., Brussels, Belgium
| | - Sylvester Pawlak
- Clinical Research Unit, Pfizer Inc., New Haven, Connecticut, USA
| | - Bruce Beckerman
- Clinical Development and Operations, Pfizer Inc., New York, New York, USA
| | - Carlos Linn
- Global Product Development, Pfizer Inc., Taipei, Taiwan
| | - Katherine Ginman
- Global Product Development, Pfizer Inc., Groton, Connecticut, USA
| | - Youliny Thay Cha
- Global Product Development, Pfizer Inc., Groton, Connecticut, USA
| | - Robert R LaBadie
- Global Product Development, Pfizer Inc., Groton, Connecticut, USA
| | - Haihong Shi
- Global Product Development, Pfizer Inc., Groton, Connecticut, USA
| | - Bharat Damle
- Global Product Development, Pfizer Inc., New York, New York, USA
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Wang B, Li HJ, Cai MM, Lin ZX, Ou XF, Wu SH, Cai RH, Wei YN, Yang F, Zhu YM, Yang ZF, Zhong NS, Lin L. Antiviral efficacy of RAY1216 monotherapy and combination therapy with ritonavir in patients with COVID-19: a phase 2, single centre, randomised, double-blind, placebo-controlled trial. EClinicalMedicine 2023; 63:102189. [PMID: 37692076 PMCID: PMC10484968 DOI: 10.1016/j.eclinm.2023.102189] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/12/2023] [Accepted: 08/15/2023] [Indexed: 09/12/2023] Open
Abstract
Background This study aimed to evaluate the efficacy and safety of RAY1216, a novel inhibitor of 3-chymotrypsin-like cysteine protease (3CLpro), in adults with coronavirus disease 2019 (COVID-19). Methods This phase 2, single centre, randomised, double-blind, placebo-controlled trial included hospitalised patients between August 14, 2022, and September 26, 2022, in Sanya Central Hospital (The Third People's Hospital of Hainan Province) in China with no severe symptoms if they had laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection for not more than 120 h (5 days) and a real-time quantitative polymerase chain reaction (qPCR) cycle threshold (Ct) value of ≤30 for both the open reading frames 1 ab (ORF1ab) and nucleocapsid (N) genes within 72 h before randomisation. Half of the participants (n = 30) were randomly assigned (2:1) to receive either RAY1216 or a matched placebo three times a day (TID) for 5 days (15 doses in total), while the other half received RAY1216 plus ritonavir (RAY1216 plus RTV) or a matched placebo every 12 h for 5 days (10 doses in total). The primary endpoint was the time of viral clearance. Secondary outcomes included the changes of the SARS-CoV-2 RNA viral load, the positivity rate of the nucleic acid test, and the recovery time of clinical symptoms. A safety evaluation was performed to record and analyse all adverse events that occurred during and after drug administration as well as any cases in which dosing was halted because of these events. Clinicaltrials.gov identifier: ChiCTR2200062889. Findings The viral shedding times in the RAY1216 and RAY1216 plus RTV groups were 166 h (95% confidence interval (CI): 140-252) and 155 h (95%CI: 131-203), respectively, which were 100 h (4.2 days) and 112 h (4.6 days) shorter than that of the placebo group, respectively (RAY1216 group vs. Placebo p = 0.0060, RAY1216 plus RTV group vs. Placebo p = 0.0001). At 24 h, 72 h, and 120 h after administration, the viral RNA loads in the RAY1216 and RAY1216 plus RTV groups were significantly less than those of the placebo groups. At 280 h (11.5 days) after administration, the nucleic acid test results in the RAY1216 and RAY1216 plus RTV groups were both negative. The common adverse events related to the investigational drugs were mild and self-limiting laboratory examination abnormalities. Interpretation Our findings suggest that RAY1216 monotherapy and RAY1216 plus ritonavir both demonstrated significant antiviral activity and reduced the duration of COVID-19 while maintaining a satisfactory safety profile. Considering the limited clinical application of RTV, it is recommended to use RAY1216 alone to further verify its efficacy and safety. Funding This study was sponsored by the Key Research and Development Program of China (2022YFC0868700).
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Affiliation(s)
- Bei Wang
- Department of Cardiology, Sanya Central Hospital (The Third People’s Hospital of Hainan Province), Sanya, Hainan 572000, PR China
| | - Hai-jun Li
- Guangdong Raynovent Biotech Co, Guangzhou, Guangdong 510700, PR China
- Department of Anatomy and Neurobiology, School of Basic Medical Science, Central South University, Changsha, Hunan 410083, PR China
| | - Mi-mi Cai
- Department of General Medicine, Sanya Central Hospital (The Third People’s Hospital of Hainan Province), Sanya, Hainan 572000, PR China
| | - Zhao-xin Lin
- Department of Neurology, Sanya Central Hospital (The Third People’s Hospital of Hainan Province), Sanya, Hainan 572000, PR China
| | - Xia-fei Ou
- Drug Clinical Trial Institution, Sanya Central Hospital (The Third People’s Hospital of Hainan Province), Sanya, Hainan 572000, PR China
| | - Shu-hua Wu
- Drug Clinical Trial Institution, Sanya Central Hospital (The Third People’s Hospital of Hainan Province), Sanya, Hainan 572000, PR China
| | - Rui-huan Cai
- Drug Clinical Trial Institution, Sanya Central Hospital (The Third People’s Hospital of Hainan Province), Sanya, Hainan 572000, PR China
| | - Ying-na Wei
- Department of Cardiology, Sanya Central Hospital (The Third People’s Hospital of Hainan Province), Sanya, Hainan 572000, PR China
| | - Fei Yang
- Department of Cardiology, Sanya Central Hospital (The Third People’s Hospital of Hainan Province), Sanya, Hainan 572000, PR China
| | - Ya-min Zhu
- Department of General Medicine, Sanya Central Hospital (The Third People’s Hospital of Hainan Province), Sanya, Hainan 572000, PR China
| | - Zi-feng Yang
- National Clinical Research Centre for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, Guangdong 510120, PR China
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, PR China
| | - Nan-shan Zhong
- National Clinical Research Centre for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, Guangdong 510120, PR China
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, PR China
| | - Ling Lin
- Department of Cardiology, Sanya Central Hospital (The Third People’s Hospital of Hainan Province), Sanya, Hainan 572000, PR China
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Chen HF, Wang WJ, Chen CY, Chang WC, Hsueh PR, Peng SL, Wu CS, Chen Y, Huang HY, Shen WJ, Wang SC, Hung MC. The natural tannins oligomeric proanthocyanidins and punicalagin are potent inhibitors of infection by SARS-CoV-2. eLife 2023; 12:e84899. [PMID: 37642993 PMCID: PMC10465125 DOI: 10.7554/elife.84899] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 07/17/2023] [Indexed: 08/31/2023] Open
Abstract
The Coronavirus Disease 2019 (COVID-19) pandemic continues to infect people worldwide. While the vaccinated population has been increasing, the rising breakthrough infection persists in the vaccinated population. For living with the virus, the dietary guidelines to prevent virus infection are worthy of and timely to develop further. Tannic acid has been demonstrated to be an effective inhibitor of coronavirus and is under clinical trial. Here we found that two other members of the tannins family, oligomeric proanthocyanidins (OPCs) and punicalagin, are also potent inhibitors against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection with different mechanisms. OPCs and punicalagin showed inhibitory activity against omicron variants of SARS-CoV-2 infection. The water extractant of the grape seed was rich in OPCs and also exhibited the strongest inhibitory activities for viral entry of wild-type and other variants in vitro. Moreover, we evaluated the inhibitory activity of grape seed extractants (GSE) supplementation against SARS-CoV-2 viral entry in vivo and observed that serum samples from the healthy human subjects had suppressive activity against different variants of SARS-CoV-2 Vpp infection after taking GSE capsules. Our results suggest that natural tannins acted as potent inhibitors against SARS-CoV-2 infection, and GSE supplementation could serve as healthy food for infection prevention.
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Affiliation(s)
- Hsiao-Fan Chen
- Graduate Institute of Biomedical Sciences, China Medical UniversityTaichungTaiwan
- Research Center for Cancer Biology, China Medical UniversityTaichungTaiwan
| | - Wei-Jan Wang
- Research Center for Cancer Biology, China Medical UniversityTaichungTaiwan
- Department of Biological Science and Technology, College of Life Sciences, China Medical UniversityTaichungTaiwan
| | - Chung-Yu Chen
- Research Center for Cancer Biology, China Medical UniversityTaichungTaiwan
| | - Wei-Chao Chang
- Center for Molecular Medicine, China Medical University Hospital, China Medical UniversityTaichungTaiwan
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, School of Medicine, China Medical UniversityTaichungTaiwan
| | - Shin-Lei Peng
- Department of Biomedical Imaging and Radiological Science, China Medical UniversityTaichungTaiwan
- Neuroscience and Brain Disease Center, China Medical UniversityTaichungTaiwan
| | - Chen-Shiou Wu
- Graduate Institute of Biomedical Sciences, China Medical UniversityTaichungTaiwan
- Research Center for Cancer Biology, China Medical UniversityTaichungTaiwan
| | - Yeh Chen
- Department of Biological Science and Technology, College of Life Sciences, China Medical UniversityTaichungTaiwan
- Institute of New Drug Development, China Medical UniversityTaichungTaiwan
| | - Hsin-Yu Huang
- Graduate Institute of Biomedical Sciences, China Medical UniversityTaichungTaiwan
| | - Wan-Jou Shen
- Graduate Institute of Biomedical Sciences, China Medical UniversityTaichungTaiwan
| | - Shao-Chun Wang
- Graduate Institute of Biomedical Sciences, China Medical UniversityTaichungTaiwan
- Research Center for Cancer Biology, China Medical UniversityTaichungTaiwan
- Center for Molecular Medicine, China Medical University Hospital, China Medical UniversityTaichungTaiwan
- Cancer Biology and Precision Therapeutics Center, China Medical UniversityTaichungTaiwan
- Department of Biotechnology, Asia UniversityTaichungTaiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, China Medical UniversityTaichungTaiwan
- Research Center for Cancer Biology, China Medical UniversityTaichungTaiwan
- Center for Molecular Medicine, China Medical University Hospital, China Medical UniversityTaichungTaiwan
- Cancer Biology and Precision Therapeutics Center, China Medical UniversityTaichungTaiwan
- Department of Biotechnology, Asia UniversityTaichungTaiwan
- Institute of Biochemistry and Molecular Biology, China Medical UniversityTaichungTaiwan
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Pojtanadithee P, Hengphasatporn K, Suroengrit A, Boonyasuppayakorn S, Wilasluck P, Deetanya P, Wangkanont K, Sukanadi IP, Chavasiri W, Wolschann P, Langer T, Shigeta Y, Maitarad P, Sanachai K, Rungrotmongkol T. Identification of Promising Sulfonamide Chalcones as Inhibitors of SARS-CoV-2 3CL pro through Structure-Based Virtual Screening and Experimental Approaches. J Chem Inf Model 2023; 63:5244-5258. [PMID: 37581276 DOI: 10.1021/acs.jcim.3c00663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
3CLpro is a viable target for developing antiviral therapies against the coronavirus. With the urgent need to find new possible inhibitors, a structure-based virtual screening approach was developed. This study recognized 75 pharmacologically bioactive compounds from our in-house library of 1052 natural product-based compounds that satisfied drug-likeness criteria and exhibited good bioavailability and membrane permeability. Among these compounds, three promising sulfonamide chalcones were identified by combined theoretical and experimental approaches, with SWC423 being the most suitable representative compound due to its competitive inhibition and low cytotoxicity in Vero E6 cells (EC50 = 0.89 ± 0.32 μM; CC50 = 25.54 ± 1.38 μM; SI = 28.70). The binding and stability of SWC423 in the 3CLpro active site were investigated through all-atom molecular dynamics simulation and fragment molecular orbital calculation, indicating its potential as a 3CLpro inhibitor for further SARS-CoV-2 therapeutic research. These findings suggested that inhibiting 3CLpro with a sulfonamide chalcone such as SWC423 may pave the effective way for developing COVID-19 treatments.
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Affiliation(s)
- Piyatida Pojtanadithee
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kowit Hengphasatporn
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Aphinya Suroengrit
- Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Siwaporn Boonyasuppayakorn
- Center of Excellence in Applied Medical Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Patcharin Wilasluck
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence for Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peerapon Deetanya
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence for Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kittikhun Wangkanont
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence for Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - I Putu Sukanadi
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Warinthorn Chavasiri
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Peter Wolschann
- Department of Pharmaceutical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
| | - Thierry Langer
- Department of Pharmaceutical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Phornphimon Maitarad
- Research Center of Nano Science and Technology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, P. R. China
| | - Kamonpan Sanachai
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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40
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Purohit P, Panda M, Muya JT, Bandyopadhyay P, Meher BR. Theoretical insights into the binding interaction of Nirmatrelvir with SARS-CoV-2 Mpro mutants (C145A and C145S): MD simulations and binding free-energy calculation to understand drug resistance. J Biomol Struct Dyn 2023:1-20. [PMID: 37599474 DOI: 10.1080/07391102.2023.2248519] [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: 03/29/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023]
Abstract
Mpro, the main protease and a crucial enzyme in SARS-CoV-2 is the most fascinating molecular target for pharmacological treatment and is also liable for viral protein maturation. For antiviral therapy, no drugs have been approved clinically to date. Targeting the Mpro with a compound having inhibitory properties against it can hinder viral replication. The therapeutic potential of the antiviral compound Nirmatrelvir (NMV) against SARS-CoV-2 Mpro was investigated using a systematic approach of molecular docking, MD simulations, and binding free energy calculation based on the MM-GBSA method. NMV, a covalent inhibitor with a recently revealed chemical structure, is a promising oral antiviral clinical candidate with significant in vitro anti-SARS-CoV-2 action in third-phase clinical trials. To explore the therapeutic ability and possible drug resistance, the Mpro system was studied for WT and two of its primary mutants (C145A & C145S). The protein-ligand (Mpro/NMV) complexes were further examined through long MD simulations to check the possible drug resistance in the mutants. To understand the binding affinity, the MM-GBSA method was applied to the Mpro/NMV complexes. Moreover, PCA analysis confirms the detachment of the linker region from the major domains in C145S and C145A mutants allowing for conformational alterations in the active-site region. Based on the predicted biological activities and binding affinities of NMV to WT and mutant (C145A & C145S) Mpro, it can be stipulated that NMV may have conventional potency to act as an anti-viral agent against WT Mpro, while the catalytic-dyad mutations may show substantial mutation-induced drug resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Madhusmita Panda
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Jules Tshishimbi Muya
- Faculte of Science, Research Centre for Theoretical Chemistry and Physics in Central Africa, University of Kinshasa, Kinshasa, Congo
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
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41
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Robinson P, Toussi SS, Aggarwal S, Bergman A, Zhu T, Hackman F, Sathish JG, Updyke L, Loudon P, Krishna G, Clevenbergh P, Hernandez-Mora MG, Cisneros Herreros JM, Albertson TE, Dougan M, Thacker A, Baniecki ML, Soares H, Whitlock M, Nucci G, Menon S, Anderson AS, Binks M. Safety, Tolerability, and Pharmacokinetics of Single and Multiple Ascending Intravenous Infusions of PF-07304814 (Lufotrelvir) in Participants Hospitalized With COVID-19. Open Forum Infect Dis 2023; 10:ofad355. [PMID: 37559753 PMCID: PMC10407246 DOI: 10.1093/ofid/ofad355] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 07/06/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND An urgent need remains for antiviral therapies to treat patients hospitalized with COVID-19. PF-07304814-the prodrug (lufotrelvir) and its active moiety (PF-00835231)-is a potent inhibitor of the SARS-CoV-2 3CL protease. METHOD Eligible participants were 18 to 79 years old and hospitalized with confirmed COVID-19. This first-in-human phase 1b study was designed with 2 groups: single ascending dose (SAD) and multiple ascending dose (MAD). Participants could receive local standard-of-care therapy. In SAD, participants were randomized to receive a 24-hour infusion of lufotrelvir/placebo. In MAD, participants were randomized to receive a 120-hour infusion of lufotrelvir/placebo. The primary endpoint was to assess the safety and tolerability of lufotrelvir. The secondary endpoint was to evaluate the pharmacokinetics of lufotrelvir and PF-00835231. RESULTS In SAD, participants were randomized to receive 250 mg lufotrelvir (n = 2), 500 mg lufotrelvir (n = 2), or placebo (n = 4) by continuous 24-hour infusion. In MAD, participants were randomized to receive 250 mg lufotrelvir (n = 7), 500 mg lufotrelvir (n = 6), or placebo (n = 4) by continuous 120-hour infusion. No adverse events or serious adverse events were considered related to lufotrelvir. At doses of 250 and 500 mg, concentrations for the prodrug lufotrelvir and active moiety PF-00835231 increased in a dose-related manner. Unbound concentrations of the lufotrelvir active metabolite reached steady state approximately 2- and 4-fold that of in vitro EC90 following 250- and 500-mg doses, respectively. CONCLUSIONS These safety and pharmacokinetic findings support the continued evaluation of lufotrelvir in clinical studies. Clinical Trials Registration. ClinicalTrials.gov NCT04535167.
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Affiliation(s)
- Philip Robinson
- Infectious Disease, Hoag Memorial Hospital Presbyterian, Newport Beach, California, USA
| | - Sima S Toussi
- Pfizer Worldwide Research, Development and Medical, Pfizer Inc, Pearl River, New York, USA
| | - Sudeepta Aggarwal
- Early Clinical Development, Pfizer Inc, Cambridge, Massachusetts, USA
| | - Arthur Bergman
- Pfizer Worldwide Research, Development and Medical, Pfizer Inc, Cambridge, Massachusetts, USA
| | - Tong Zhu
- Pfizer Worldwide Research, Development and Medical, Pfizer Inc, Cambridge, Massachusetts, USA
| | - Frances Hackman
- Pfizer Worldwide Research, Development and Medical, Pfizer Ltd, Cambridge, UK
| | - Jean G Sathish
- Drug Safety Unit, Pfizer Inc, Pearl River, New York, USA
| | | | | | | | | | | | | | | | - Michael Dougan
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | | | - Holly Soares
- Early Clinical Development, Pfizer Inc, Cambridge, Massachusetts, USA
| | - Mark Whitlock
- Early Clinical Development, Pfizer Inc, Cambridge, UK
| | - Gianluca Nucci
- Pfizer Worldwide Research, Development and Medical, Pfizer Ltd, Cambridge, UK
| | - Sandeep Menon
- Pfizer Worldwide Research, Development and Medical, Pfizer Ltd, Cambridge, UK
| | | | - Michael Binks
- Pfizer Worldwide Research, Development and Medical, Pfizer Ltd, Cambridge, UK
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42
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Hetmann M, Langner C, Durmaz V, Cespugli M, Köchl K, Krassnigg A, Blaschitz K, Groiss S, Loibner M, Ruau D, Zatloukal K, Gruber K, Steinkellner G, Gruber CC. Identification and validation of fusidic acid and flufenamic acid as inhibitors of SARS-CoV-2 replication using DrugSolver CavitomiX. Sci Rep 2023; 13:11783. [PMID: 37479788 PMCID: PMC10362000 DOI: 10.1038/s41598-023-39071-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/19/2023] [Indexed: 07/23/2023] Open
Abstract
In this work, we present DrugSolver CavitomiX, a novel computational pipeline for drug repurposing and identifying ligands and inhibitors of target enzymes. The pipeline is based on cavity point clouds representing physico-chemical properties of the cavity induced solely by the protein. To test the pipeline's ability to identify inhibitors, we chose enzymes essential for SARS-CoV-2 replication as a test system. The active-site cavities of the viral enzymes main protease (Mpro) and papain-like protease (Plpro), as well as of the human transmembrane serine protease 2 (TMPRSS2), were selected as target cavities. Using active-site point-cloud comparisons, it was possible to identify two compounds-flufenamic acid and fusidic acid-which show strong inhibition of viral replication. The complexes from which fusidic acid and flufenamic acid were derived would not have been identified using classical sequence- and structure-based methods as they show very little structural (TM-score: 0.1 and 0.09, respectively) and very low sequence (~ 5%) identity to Mpro and TMPRSS2, respectively. Furthermore, a cavity-based off-target screening was performed using acetylcholinesterase (AChE) as an example. Using cavity comparisons, the human carboxylesterase was successfully identified, which is a described off-target for AChE inhibitors.
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Affiliation(s)
- M Hetmann
- Innophore, San Francisco, CA, USA
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - C Langner
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - V Durmaz
- Innophore, San Francisco, CA, USA
| | | | - K Köchl
- Innophore, San Francisco, CA, USA
| | | | | | - S Groiss
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - M Loibner
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - D Ruau
- NVIDIA, Santa Clara, CA, USA
| | - K Zatloukal
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - K Gruber
- Innophore, San Francisco, CA, USA
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - G Steinkellner
- Innophore, San Francisco, CA, USA
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - C C Gruber
- Innophore, San Francisco, CA, USA.
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.
- Austrian Centre of Industrial Biotechnology, Graz, Austria.
- Field of Excellence BioHealth - University of Graz, Graz, Austria.
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43
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She Z, Yao Y, Wang C, Li Y, Xiong X, Liu Y. M pro-targeted anti-SARS-CoV-2 inhibitor-based drugs. JOURNAL OF CHEMICAL RESEARCH 2023; 47:17475198231184799. [PMID: 37455837 PMCID: PMC10333551 DOI: 10.1177/17475198231184799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 is a global health emergency. The main protease is an important drug target in coronaviruses. It plays an important role in the processing of viral RNA-translated polyproteins and is highly conserved in the amino acid sequence and three-dimensional structure, making it a good drug target for which several small molecule inhibitors are available. This paper describes the various anti-severe acute respiratory syndrome coronavirus 2 inhibitor drugs targeting Mpro discovered since the severe acute respiratory syndrome coronavirus 2 outbreak at the end of 2019, with all these compounds inhibiting severe acute respiratory syndrome coronavirus 2 Mpro activity in vitro. This provides a reference for the development of severe acute respiratory syndrome coronavirus 2 Mpro-targeted inhibitors and the design of therapeutic approaches to address newly emerged severe acute respiratory syndrome coronavirus 2 mutant strains with immune evasion capabilities.
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Affiliation(s)
- Zhuxin She
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, P.R. China
| | - Yinuo Yao
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, P.R. China
| | - Conglong Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, P.R. China
| | - Yi Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, P.R. China
| | - Xiaohui Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, P.R. China
| | - Yuanyuan Liu
- School of Pharmaceutical and Chemical Engineering, ChengXian College, Southeast University, Nanjing, P.R. China
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44
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Castillo-Campos L, Velázquez-Libera JL, Caballero J. Computational study of the binding orientation and affinity of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-1 considering the protein flexibility by using molecular dynamics and cross-docking. Front Mol Biosci 2023; 10:1215499. [PMID: 37426421 PMCID: PMC10326900 DOI: 10.3389/fmolb.2023.1215499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
The papain-like protease (PLpro) from zoonotic coronaviruses (CoVs) has been identified as a target with an essential role in viral respiratory diseases caused by Severe Acute Respiratory Syndrome-associated coronaviruses (SARS-CoVs). The design of PLpro inhibitors has been proposed as an alternative to developing potential drugs against this disease. In this work, 67 naphthalene-derived compounds as noncovalent PLpro inhibitors were studied using molecular modeling methods. Structural characteristics of the bioactive conformations of these inhibitors and their interactions at the SARS-CoV-1 PLpro binding site were reported here in detail, taking into account the flexibility of the protein residues. Firstly, a molecular docking protocol was used to obtain the orientations of the inhibitors. After this, the orientations were compared, and the recurrent interactions between the PLpro residues and ligand chemical groups were described (with LigRMSD and interaction fingerprints methods). In addition, efforts were made to find correlations between docking energy values and experimentally determined binding affinities. For this, the PLpro was sampled by using Gaussian Accelerated Molecular Dynamics (GaMD), generating multiple conformations of the binding site. Diverse protein conformations were selected and a cross-docking experiment was performed, yielding models of the 67 naphthalene-derived compounds adopting different binding modes. Representative complexes for each ligand were selected to obtain the highest correlation between docking energies and activities. A good correlation (R 2 = 0.948) was found when this flexible docking protocol was performed.
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45
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Shehzadi K, Saba A, Yu M, Liang J. Structure-Based Drug Design of RdRp Inhibitors against SARS-CoV-2. Top Curr Chem (Cham) 2023; 381:22. [PMID: 37318607 DOI: 10.1007/s41061-023-00432-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide pandemic since 2019, spreading rapidly and posing a significant threat to human health and life. With over 6 billion confirmed cases of the virus, the need for effective therapeutic drugs has become more urgent than ever before. RNA-dependent RNA polymerase (RdRp) is crucial in viral replication and transcription, catalysing viral RNA synthesis and serving as a promising therapeutic target for developing antiviral drugs. In this article, we explore the inhibition of RdRp as a potential treatment for viral diseases, analysing the structural information of RdRp in virus proliferation and summarizing the reported inhibitors' pharmacophore features and structure-activity relationship profiles. We hope that the information provided by this review will aid in structure-based drug design and aid in the global fight against SARS-CoV-2 infection.
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Affiliation(s)
- Kiran Shehzadi
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Afsheen Saba
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Mingjia Yu
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
| | - Jianhua Liang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
- Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing, 314019, China.
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46
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Zmudzinski M, Rut W, Olech K, Granda J, Giurg M, Burda-Grabowska M, Kaleta R, Zgarbova M, Kasprzyk R, Zhang L, Sun X, Lv Z, Nayak D, Kesik-Brodacka M, Olsen SK, Weber J, Hilgenfeld R, Jemielity J, Drag M. Ebselen derivatives inhibit SARS-CoV-2 replication by inhibition of its essential proteins: PL pro and M pro proteases, and nsp14 guanine N7-methyltransferase. Sci Rep 2023; 13:9161. [PMID: 37280236 DOI: 10.1038/s41598-023-35907-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/25/2023] [Indexed: 06/08/2023] Open
Abstract
Proteases encoded by SARS-CoV-2 constitute a promising target for new therapies against COVID-19. SARS-CoV-2 main protease (Mpro, 3CLpro) and papain-like protease (PLpro) are responsible for viral polyprotein cleavage-a process crucial for viral survival and replication. Recently it was shown that 2-phenylbenzisoselenazol-3(2H)-one (ebselen), an organoselenium anti-inflammatory small-molecule drug, is a potent, covalent inhibitor of both the proteases and its potency was evaluated in enzymatic and antiviral assays. In this study, we screened a collection of 34 ebselen and ebselen diselenide derivatives for SARS-CoV-2 PLpro and Mpro inhibitors. Our studies revealed that ebselen derivatives are potent inhibitors of both the proteases. We identified three PLpro and four Mpro inhibitors superior to ebselen. Independently, ebselen was shown to inhibit the N7-methyltransferase activity of SARS-CoV-2 nsp14 protein involved in viral RNA cap modification. Hence, selected compounds were also evaluated as nsp14 inhibitors. In the second part of our work, we employed 11 ebselen analogues-bis(2-carbamoylaryl)phenyl diselenides-in biological assays to evaluate their anti-SARS-CoV-2 activity in Vero E6 cells. We present their antiviral and cytoprotective activity and also low cytotoxicity. Our work shows that ebselen, its derivatives, and diselenide analogues constitute a promising platform for development of new antivirals targeting the SARS-CoV-2 virus.
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Affiliation(s)
- Mikolaj Zmudzinski
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Kamila Olech
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Jarosław Granda
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Mirosław Giurg
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Małgorzata Burda-Grabowska
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Rafał Kaleta
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Michala Zgarbova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague, Czech Republic
| | - Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Linlin Zhang
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Zongyang Lv
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Digant Nayak
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | | | - Shaun K Olsen
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague, Czech Republic
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562, Lübeck, Germany
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
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47
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Farkaš B, Minneci M, Misevicius M, Rozas I. A Tale of Two Proteases: M Pro and TMPRSS2 as Targets for COVID-19 Therapies. Pharmaceuticals (Basel) 2023; 16:834. [PMID: 37375781 DOI: 10.3390/ph16060834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Considering the importance of the 2019 outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulting in the coronavirus disease 2019 (COVID-19) pandemic, an overview of two proteases that play an important role in the infection by SARS-CoV-2, the main protease of SARS-CoV-2 (MPro) and the host transmembrane protease serine 2 (TMPRSS2), is presented in this review. After summarising the viral replication cycle to identify the relevance of these proteases, the therapeutic agents already approved are presented. Then, this review discusses some of the most recently reported inhibitors first for the viral MPro and next for the host TMPRSS2 explaining the mechanism of action of each protease. Afterward, some computational approaches to design novel MPro and TMPRSS2 inhibitors are presented, also describing the corresponding crystallographic structures reported so far. Finally, a brief discussion on a few reports found some dual-action inhibitors for both proteases is given. This review provides an overview of two proteases of different origins (viral and human host) that have become important targets for the development of antiviral agents to treat COVID-19.
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Affiliation(s)
- Barbara Farkaš
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02 R590 Dublin, Ireland
| | - Marco Minneci
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02 R590 Dublin, Ireland
| | - Matas Misevicius
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02 R590 Dublin, Ireland
| | - Isabel Rozas
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, D02 R590 Dublin, Ireland
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48
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Ranard BL, Chow CC, Megjhani M, Asgari S, Park S, Vodovotz Y. A mathematical model of SARS-CoV-2 immunity predicts paxlovid rebound. J Med Virol 2023; 95:e28854. [PMID: 37287404 PMCID: PMC10264150 DOI: 10.1002/jmv.28854] [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: 02/22/2023] [Revised: 05/07/2023] [Accepted: 05/25/2023] [Indexed: 06/09/2023]
Abstract
Nirmatrelvir/ritonavir (Paxlovid), an oral antiviral medication targeting SARS-CoV-2, remains an important treatment for COVID-19. Initial studies of nirmatrelvir/ritonavir were performed in SARS-CoV-2 unvaccinated patients without prior confirmed SARS-CoV-2 infection; however, most individuals have now either been vaccinated and/or have experienced SARS-CoV-2 infection. After nirmatrelvir/ritonavir became widely available, reports surfaced of "Paxlovid rebound," a phenomenon in which symptoms (and SARS-CoV-2 test positivity) would initially resolve, but after finishing treatment, symptoms and test positivity would return. We used a previously described parsimonious mathematical model of immunity to SARS-CoV-2 infection to model the effect of nirmatrelvir/ritonavir treatment in unvaccinated and vaccinated patients. Model simulations show that viral rebound after treatment occurs only in vaccinated patients, while unvaccinated (SARS-COV-2 naïve) patients treated with nirmatrelvir/ritonavir do not experience any rebound in viral load. This work suggests that an approach combining parsimonious models of the immune system could be used to gain important insights in the context of emerging pathogens.
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Affiliation(s)
- Benjamin L. Ranard
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, Columbia University / Columbia University Irving Medical Center/ NewYork-Presbyterian, New York, NY
- Program for Hospital and Intensive Care Informatics, Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Carson C. Chow
- Mathematical Biology Section, Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD
| | - Murad Megjhani
- Program for Hospital and Intensive Care Informatics, Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Shadnaz Asgari
- Department of Biomedical Engineering, California State University, Long Beach, California, United States of America, Department of Computer Engineering and Computer Science, California State University, Long Beach, California, United States of America
| | - Soojin Park
- Program for Hospital and Intensive Care Informatics, Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
- Department of Neurology & Division of Critical Care and Hospitalist Neurology, Columbia University Vagelos College of Physicians and Surgeons, Columbia University / Columbia University Irving Medical Center/ NewYork-Presbyterian, New York, NY
- Department of Biomedical Informatics, Columbia University Vagelos College of Physicians and Surgeons, Columbia University / Columbia University Irving Medical Center/ NewYork-Presbyterian, New York, NY
| | - Yoram Vodovotz
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA
- Center for Inflammation and Regeneration Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Systems Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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49
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Yang H, You M, Shu X, Zhen J, Zhu M, Fu T, Zhang Y, Jiang X, Zhang L, Xu Y, Zhang Y, Su H, Zhang Q, Shen J. Design, synthesis and biological evaluation of peptidomimetic benzothiazolyl ketones as 3CL pro inhibitors against SARS-CoV-2. Eur J Med Chem 2023; 257:115512. [PMID: 37253309 DOI: 10.1016/j.ejmech.2023.115512] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 05/01/2023] [Accepted: 05/22/2023] [Indexed: 06/01/2023]
Abstract
A series of peptidomimetic compounds containing benzothiazolyl ketone and [2.2.1] azabicyclic ring was designed, synthesized and evaluated in the hope of obtaining potent oral 3CLpro inhibitors with improved pharmacokinetic properties. Among the target compounds, 11b had the best enzymatic potency (IC50 = 0.110 μM) and 11e had the best microsomal stability (t1/2 > 120 min) and good enzyme activity (IC50 = 0.868 μM). Therefore, compounds 11b and 11e were chosen for further evaluation of pharmacokinetics in ICR mice. The results exhibited that the AUC(0-t) of 11e was 5143 h*ng/mL following single-dose oral administration of 20 mg/kg, and the F was 67.98%. Further structural modification was made to obtain compounds 11g-11j based on 11e. Among them, 11j exhibited the best enzyme inhibition activity against SARS-CoV-2 3CLpro (IC50 = 1.646 μM), the AUC(0-t) was 32473 h*ng/mL (20 mg/kg, po), and the F was 48.1%. In addition, 11j displayed significant anti-SARS-CoV-2 activity (EC50 = 0.18 μM) and low cytotoxicity (CC50 > 50 μM) in Vero E6 cells. All of the above results suggested that compound 11j was a promising lead compound in the development of oral 3CLpro inhibitors and deserved further research.
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Affiliation(s)
- Hanxi Yang
- College of Chemistry, Zhengzhou University, 100 Kexuedadao Road, Zhengzhou, 450001, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Mengyuan You
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xiaoyang Shu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Jingyao Zhen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, PR China
| | - Mengwei Zhu
- College of Pharmacy, An Hui University of Traditional Chinese Medicine, Hefei, 230012, China; Yangtze Delta Drug Advanced Research Institute and Yangtze Delta Pharmaceutical College, Nantong, 226133, China
| | - Tiantian Fu
- College of Pharmacy, An Hui University of Traditional Chinese Medicine, Hefei, 230012, China; Yangtze Delta Drug Advanced Research Institute and Yangtze Delta Pharmaceutical College, Nantong, 226133, China
| | - Yan Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiangrui Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, PR China
| | - Leike Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China; Hubei Jiangxia Laboratory, Wuhan, 430200, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yumin Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China.
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Qiumeng Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Jingshan Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
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50
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Chen S, Arutyunova E, Lu J, Khan MB, Rut W, Zmudzinski M, Shahbaz S, Iyyathurai J, Moussa EW, Turner Z, Bai B, Lamer T, Nieman JA, Vederas JC, Julien O, Drag M, Elahi S, Young HS, Lemieux MJ. SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals. ACS CENTRAL SCIENCE 2023; 9:696-708. [PMID: 37122453 PMCID: PMC10042146 DOI: 10.1021/acscentsci.3c00054] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Indexed: 05/03/2023]
Abstract
The main protease of SARS-CoV-2 (Mpro) is the most promising drug target against coronaviruses due to its essential role in virus replication. With newly emerging variants there is a concern that mutations in Mpro may alter the structural and functional properties of protease and subsequently the potency of existing and potential antivirals. We explored the effect of 31 mutations belonging to 5 variants of concern (VOCs) on catalytic parameters and substrate specificity, which revealed changes in substrate binding and the rate of cleavage of a viral peptide. Crystal structures of 11 Mpro mutants provided structural insight into their altered functionality. Additionally, we show Mpro mutations influence proteolysis of an immunomodulatory host protein Galectin-8 (Gal-8) and a subsequent significant decrease in cytokine secretion, providing evidence for alterations in the escape of host-antiviral mechanisms. Accordingly, mutations associated with the Gamma VOC and highly virulent Delta VOC resulted in a significant increase in Gal-8 cleavage. Importantly, IC50s of nirmatrelvir (Pfizer) and our irreversible inhibitor AVI-8053 demonstrated no changes in potency for both drugs for all mutants, suggesting Mpro will remain a high-priority antiviral drug candidate as SARS-CoV-2 evolves.
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Affiliation(s)
- Sizhu
Amelia Chen
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Elena Arutyunova
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jimmy Lu
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Muhammad Bashir Khan
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Wioletta Rut
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Mikolaj Zmudzinski
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shima Shahbaz
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jegan Iyyathurai
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Eman W. Moussa
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Zoe Turner
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Bing Bai
- Li
Ka Shing Applied Virology Institute, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Tess Lamer
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - James A. Nieman
- Li
Ka Shing Applied Virology Institute, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - John C. Vederas
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Marcin Drag
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shokrollah Elahi
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Howard S. Young
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - M. Joanne Lemieux
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
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