1
|
Dos Santos Nascimento IJ, Gomes JNS, de Oliveira Viana J, de Medeiros E Silva YMS, Barbosa EG, de Moura RO. The Power of Molecular Dynamics Simulations and Their Applications to Discover Cysteine Protease Inhibitors. Mini Rev Med Chem 2024; 24:1125-1146. [PMID: 37680157 DOI: 10.2174/1389557523666230901152257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 06/15/2023] [Accepted: 07/18/2023] [Indexed: 09/09/2023]
Abstract
A large family of enzymes with the function of hydrolyzing peptide bonds, called peptidases or cysteine proteases (CPs), are divided into three categories according to the peptide chain involved. CPs catalyze the hydrolysis of amide, ester, thiol ester, and thioester peptide bonds. They can be divided into several groups, such as papain-like (CA), viral chymotrypsin-like CPs (CB), papainlike endopeptidases of RNA viruses (CC), legumain-type caspases (CD), and showing active residues of His, Glu/Asp, Gln, Cys (CE). The catalytic mechanism of CPs is the essential cysteine residue present in the active site. These mechanisms are often studied through computational methods that provide new information about the catalytic mechanism and identify inhibitors. The role of computational methods during drug design and development stages is increasing. Methods in Computer-Aided Drug Design (CADD) accelerate the discovery process, increase the chances of selecting more promising molecules for experimental studies, and can identify critical mechanisms involved in the pathophysiology and molecular pathways of action. Molecular dynamics (MD) simulations are essential in any drug discovery program due to their high capacity for simulating a physiological environment capable of unveiling significant inhibition mechanisms of new compounds against target proteins, especially CPs. Here, a brief approach will be shown on MD simulations and how the studies were applied to identify inhibitors or critical information against cysteine protease from several microorganisms, such as Trypanosoma cruzi (cruzain), Trypanosoma brucei (rhodesain), Plasmodium spp. (falcipain), and SARS-CoV-2 (Mpro). We hope the readers will gain new insights and use our study as a guide for potential compound identifications using MD simulations.
Collapse
Affiliation(s)
- Igor José Dos Santos Nascimento
- Department of Pharmacy, Cesmac University Center, Maceió, 57051-160, Brazil
- Department of Pharmacy, Drug Development and Synthesis Laboratory, State University of Paraíba, Campina Grande, 58429-500, Brazil
- Postgraduate Program in Pharmaceutical Sciences, State University of Paraíba, Campina Grande, 58429-500, Brazil
| | - Joilly Nilce Santana Gomes
- Department of Pharmacy, Drug Development and Synthesis Laboratory, State University of Paraíba, Campina Grande, 58429-500, Brazil
| | - Jéssika de Oliveira Viana
- Post-graduate Program in Bioinformatics, Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Yvnni Maria Sales de Medeiros E Silva
- Department of Pharmacy, Drug Development and Synthesis Laboratory, State University of Paraíba, Campina Grande, 58429-500, Brazil
- Postgraduate Program in Pharmaceutical Sciences, State University of Paraíba, Campina Grande, 58429-500, Brazil
| | - Euzébio Guimarães Barbosa
- Post-graduate Program in Bioinformatics, Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil
- Post-graduate Program in Pharmaceutical Sciences, Faculty of Pharmacy, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Ricardo Olimpio de Moura
- Department of Pharmacy, Drug Development and Synthesis Laboratory, State University of Paraíba, Campina Grande, 58429-500, Brazil
- Post-graduate Program in Pharmaceutical Sciences, State University of Paraíba, Campina Grande 58429-500, Brazil
| |
Collapse
|
2
|
Ferreiro D, Khalil R, Gallego MJ, Osorio NS, Arenas M. The evolution of the HIV-1 protease folding stability. Virus Evol 2022; 8:veac115. [PMID: 36601299 PMCID: PMC9802575 DOI: 10.1093/ve/veac115] [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: 07/20/2022] [Revised: 10/10/2022] [Accepted: 12/03/2022] [Indexed: 12/11/2022] Open
Abstract
The evolution of structural proteins is generally constrained by the folding stability. However, little is known about the particular capacity of viral proteins to accommodate mutations that can potentially affect the protein stability and, in general, the evolution of the protein stability over time. As an illustrative model case, here, we investigated the evolution of the stability of the human immunodeficiency virus (HIV-1) protease (PR), which is a common HIV-1 drug target, under diverse evolutionary scenarios that include (1) intra-host virus evolution in a cohort of seventy-five patients sampled over time, (2) intra-host virus evolution sampled before and after specific PR-based treatments, and (3) inter-host evolution considering extant and ancestral (reconstructed) PR sequences from diverse HIV-1 subtypes. We also investigated the specific influence of currently known HIV-1 PR resistance mutations on the PR folding stability. We found that the HIV-1 PR stability fluctuated over time within a constant and wide range in any studied evolutionary scenario, accommodating multiple mutations that partially affected the stability while maintaining activity. We did not identify relationships between change of PR stability and diverse clinical parameters such as viral load, CD4+ T-cell counts, and a surrogate of time from infection. Counterintuitively, we predicted that nearly half of the studied HIV-1 PR resistance mutations do not significantly decrease stability, which, together with compensatory mutations, would allow the protein to adapt without requiring dramatic stability changes. We conclude that the HIV-1 PR presents a wide structural plasticity to acquire molecular adaptations without affecting the overall evolution of stability.
Collapse
Affiliation(s)
- David Ferreiro
- CINBIO, Universidade de Vigo, Vigo 36310, Spain,Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo 36310, Spain
| | - Ruqaiya Khalil
- CINBIO, Universidade de Vigo, Vigo 36310, Spain,Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo 36310, Spain
| | - María J Gallego
- CINBIO, Universidade de Vigo, Vigo 36310, Spain,Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo 36310, Spain
| | - Nuno S Osorio
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga 4710-057, Portugal,ICVS/3Bs—PT Government Associate Laboratory, Guimarães 4806-909, Portugal
| | | |
Collapse
|
3
|
Rahmah L, Abarikwu SO, Arero AG, Essouma M, Jibril AT, Fal A, Flisiak R, Makuku R, Marquez L, Mohamed K, Ndow L, Zarębska-Michaluk D, Rezaei N, Rzymski P. Oral antiviral treatments for COVID-19: opportunities and challenges. Pharmacol Rep 2022; 74:1255-1278. [PMID: 35871712 PMCID: PMC9309032 DOI: 10.1007/s43440-022-00388-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/24/2022] [Accepted: 07/06/2022] [Indexed: 01/18/2023]
Abstract
The use of antiviral COVID-19 medications can successfully inhibit SARS-CoV-2 replication and prevent disease progression to a more severe form. However, the timing of antiviral treatment plays a crucial role in this regard. Oral antiviral drugs provide an opportunity to manage SARS-CoV-2 infection without a need for hospital admission, easing the general burden that COVID-19 can have on the healthcare system. This review paper (i) presents the potential pharmaceutical antiviral targets, including various host-based targets and viral-based targets, (ii) characterizes the first-generation anti-SARS-CoV-2 oral drugs (nirmatrelvir/ritonavir and molnupiravir), (iii) summarizes the clinical progress of other oral antivirals for use in COVID-19, (iv) discusses ethical issues in such clinical trials and (v) presents challenges associated with the use of oral antivirals in clinical practice. Oral COVID-19 antivirals represent a part of the strategy to adapt to long-term co-existence with SARS-CoV-2 in a manner that prevents healthcare from being overwhelmed. It is pivotal to ensure equal and fair global access to the currently available oral antivirals and those authorized in the future.
Collapse
Affiliation(s)
- Laila Rahmah
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran ,Universal Scientific Education and Research Network (USERN), Jakarta, Indonesia
| | - Sunny O. Abarikwu
- Department of Biochemistry, University of Port Harcourt, Choba, Nigeria ,Universal Scientific Education and Research Network (USERN), Choba, Nigeria
| | - Amanuel Godana Arero
- Cardiac Primary Prevention Research Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran ,Universal Scientific Education and Research Network (USERN), Addis Ababa, Ethiopia
| | - Mickael Essouma
- Department of Internal Medicine and Specialties, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon ,Universal Scientific Education and Research Network, Yaoundé, Cameroon
| | - Aliyu Tijani Jibril
- Department of Community Nutrition, School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences, Tehran, Iran ,Nutritional and Health Team (NHT), Universal Scientific Education and Research Network (USERN), Tehran, Iran ,Universal Scientific Education and Research Network (USERN), Accra, Ghana
| | - Andrzej Fal
- Department of Population Health, Division of Public Health, Wroclaw Medical University, Wroclaw, Poland ,Collegium Medicum, Warsaw Faculty of Medicine, Cardinal Stefan Wyszyński University, Warsaw, Poland ,Integrated Science Association (ISA), Universal Scientific Education and Research Network (USERN), Poznań, Poland
| | - Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, Białystok, Poland
| | - Rangarirai Makuku
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran ,Universal Scientific Education and Research Network (USERN), Harare, Zimbabwe
| | - Leander Marquez
- College of Social Sciences and Philosophy, University of the Philippines Diliman, Quezon City, Philippines ,Education and Research Network (USERN), Universal Scientific, Quezon City, Philippines
| | - Kawthar Mohamed
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran ,Universal Scientific Education and Research Network (USERN), Manama, Bahrain
| | - Lamin Ndow
- National Health Laboratory Service, Kotu, Gambia ,Universal Scientific Education and Research Network (USERN), Banjul, Gambia
| | | | - Nima Rezaei
- Research Center for Immunodeficiencies, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran ,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran ,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Piotr Rzymski
- Integrated Science Association (ISA), Universal Scientific Education and Research Network (USERN), Poznań, Poland ,Department of Environmental Medicine, Poznan University of Medical Sciences, Poznań, Poland
| |
Collapse
|
4
|
Ayele AG, Enyew EF, Kifle ZD. Roles of existing drug and drug targets for COVID-19 management. Metabol Open 2021; 11:100103. [PMID: 34222852 PMCID: PMC8239316 DOI: 10.1016/j.metop.2021.100103] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 06/27/2021] [Indexed: 02/07/2023] Open
Abstract
In December 2019, a highly transmissible, pneumonia epidemic caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), erupted in China and other countries, resulting in devastation and health crisis worldwide currently. The search and using existing drugs support to curb the current highly contagious viral infection is spirally increasing since the pandemic began. This is based on these drugs had against other related RNA-viruses such as MERS-Cov, and SARS-Cov. Moreover, researchers are scrambling to identify novel drug targets and discover novel therapeutic options to vanquish the current pandemic. Since there is no definitive treatment to control Covid-19 vaccines are remain to be a lifeline. Currently, many vaccine candidates are being developed with most of them are reported to have positive results. Therapeutic targets such as helicases, transmembrane serine protease 2, cathepsin L, cyclin G-associated kinase, adaptor-associated kinase 1, two-pore channel, viral virulence factors, 3-chymotrypsin-like protease, suppression of excessive inflammatory response, inhibition of viral membrane, nucleocapsid, envelope, and accessory proteins, and inhibition of endocytosis were identified as a potential target against COVID-19 infection. This review also summarizes plant-based medicines for the treatment of COVID-19 such as saposhnikoviae divaricata, lonicerae japonicae flos, scutellaria baicalensis, lonicera japonicae, and some others. Thus, this review aimed to focus on the most promising therapeutic targets being repurposed against COVID-19 and viral elements that are used in COVID-19 vaccine candidates.
Collapse
Key Words
- 3CLpro, 3-chymotrypsin-like protease
- AAK1, adaptor-associated kinase 1
- ACE-2, Angiotensin-Converting Enzyme-2
- CEF, Cepharanthine
- COVID-19
- COVID-19, coronavirus disease-2019
- Existing drug
- GAK, cyclin G-associated kinase
- MERS-CoV, Middle East respiratory syndrome coronavirus
- Management
- Nsp, non-structure protein
- ORF, open reading frame
- PLpro, papain-like protease
- RdRp, RNA-dependence RNA-polymerase
- SARS-COV-2, severe acute respiratory syndrome coronavirus-2
- TMPRSS2, transmembrane Serine Protease 2
- TPC2, two-pore channel 2
- Therapeutic target
Collapse
Affiliation(s)
- Akeberegn Gorems Ayele
- Department of Pharmacology and Clinical Pharmacy, School of Pharmacy, College of Health Science, Addis Ababa University, Addis Ababa, Ethiopia
| | - Engidaw Fentahun Enyew
- Department of Human Anatomy, School of Medicine, College of Medicine and Health Sciences, Gondar, Ethiopia
| | - Zemene Demelash Kifle
- Department of Pharmacology, School of Pharmacy, College of Medicine and Health Science, University of Gondar, Gondar, Ethiopia
| |
Collapse
|
5
|
Waman VP, Sen N, Varadi M, Daina A, Wodak SJ, Zoete V, Velankar S, Orengo C. The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. Brief Bioinform 2021; 22:742-768. [PMID: 33348379 PMCID: PMC7799268 DOI: 10.1093/bib/bbaa362] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 01/18/2023] Open
Abstract
SARS-CoV-2 is the causative agent of COVID-19, the ongoing global pandemic. It has posed a worldwide challenge to human health as no effective treatment is currently available to combat the disease. Its severity has led to unprecedented collaborative initiatives for therapeutic solutions against COVID-19. Studies resorting to structure-based drug design for COVID-19 are plethoric and show good promise. Structural biology provides key insights into 3D structures, critical residues/mutations in SARS-CoV-2 proteins, implicated in infectivity, molecular recognition and susceptibility to a broad range of host species. The detailed understanding of viral proteins and their complexes with host receptors and candidate epitope/lead compounds is the key to developing a structure-guided therapeutic design. Since the discovery of SARS-CoV-2, several structures of its proteins have been determined experimentally at an unprecedented speed and deposited in the Protein Data Bank. Further, specialized structural bioinformatics tools and resources have been developed for theoretical models, data on protein dynamics from computer simulations, impact of variants/mutations and molecular therapeutics. Here, we provide an overview of ongoing efforts on developing structural bioinformatics tools and resources for COVID-19 research. We also discuss the impact of these resources and structure-based studies, to understand various aspects of SARS-CoV-2 infection and therapeutic development. These include (i) understanding differences between SARS-CoV-2 and SARS-CoV, leading to increased infectivity of SARS-CoV-2, (ii) deciphering key residues in the SARS-CoV-2 involved in receptor-antibody recognition, (iii) analysis of variants in host proteins that affect host susceptibility to infection and (iv) analyses facilitating structure-based drug and vaccine design against SARS-CoV-2.
Collapse
Affiliation(s)
| | | | | | - Antoine Daina
- Molecular Modeling Group at SIB, Swiss Institute of Bioinformatics
| | | | - Vincent Zoete
- Department of Fundamental Oncology at the University of Lausanne and Group leader at SIB
| | | | | |
Collapse
|
6
|
Gil C, Ginex T, Maestro I, Nozal V, Barrado-Gil L, Cuesta-Geijo MÁ, Urquiza J, Ramírez D, Alonso C, Campillo NE, Martinez A. COVID-19: Drug Targets and Potential Treatments. J Med Chem 2020; 63:12359-12386. [PMID: 32511912 PMCID: PMC7323060 DOI: 10.1021/acs.jmedchem.0c00606] [Citation(s) in RCA: 283] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Indexed: 02/07/2023]
Abstract
Currently, humans are immersed in a pandemic caused by the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which threatens public health worldwide. To date, no drug or vaccine has been approved to treat the severe disease caused by this coronavirus, COVID-19. In this paper, we will focus on the main virus-based and host-based targets that can guide efforts in medicinal chemistry to discover new drugs for this devastating disease. In principle, all CoV enzymes and proteins involved in viral replication and the control of host cellular machineries are potentially druggable targets in the search for therapeutic options for SARS-CoV-2. This Perspective provides an overview of the main targets from a structural point of view, together with reported therapeutic compounds with activity against SARS-CoV-2 and/or other CoVs. Also, the role of innate immune response to coronavirus infection and the related therapeutic options will be presented.
Collapse
Affiliation(s)
- Carmen Gil
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Tiziana Ginex
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Inés Maestro
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Vanesa Nozal
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Lucía Barrado-Gil
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Miguel Ángel Cuesta-Geijo
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Jesús Urquiza
- Department of Biotechnology,
Instituto Nacional de Investigación y
Tecnología Agraria y Alimentaria (INIA),
Ctra. de la Coruña km 7.5, 28040 Madrid,
Spain
| | - David Ramírez
- Instituto de Ciencias Biomédicas,
Universidad Autónoma de Chile,
Llano Subercaseaux 2801- piso 6, 7500912 Santiago,
Chile
| | - Covadonga Alonso
- Department of Biotechnology,
Instituto Nacional de Investigación y
Tecnología Agraria y Alimentaria (INIA),
Ctra. de la Coruña km 7.5, 28040 Madrid,
Spain
| | - Nuria E. Campillo
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Ana Martinez
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| |
Collapse
|
7
|
De Pasquale V, Moles A, Pavone LM. Cathepsins in the Pathophysiology of Mucopolysaccharidoses: New Perspectives for Therapy. Cells 2020; 9:cells9040979. [PMID: 32326609 PMCID: PMC7227001 DOI: 10.3390/cells9040979] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 02/07/2023] Open
Abstract
Cathepsins (CTSs) are ubiquitously expressed proteases normally found in the endolysosomal compartment where they mediate protein degradation and turnover. However, CTSs are also found in the cytoplasm, nucleus, and extracellular matrix where they actively participate in cell signaling, protein processing, and trafficking through the plasma and nuclear membranes and between intracellular organelles. Dysregulation in CTS expression and/or activity disrupts cellular homeostasis, thus contributing to many human diseases, including inflammatory and cardiovascular diseases, neurodegenerative disorders, diabetes, obesity, cancer, kidney dysfunction, and others. This review aimed to highlight the involvement of CTSs in inherited lysosomal storage disorders, with a primary focus to the emerging evidence on the role of CTSs in the pathophysiology of Mucopolysaccharidoses (MPSs). These latter diseases are characterized by severe neurological, skeletal and cardiovascular phenotypes, and no effective cure exists to date. The advance in the knowledge of the molecular mechanisms underlying the activity of CTSs in MPSs may open a new challenge for the development of novel therapeutic approaches for the cure of such intractable diseases.
Collapse
Affiliation(s)
- Valeria De Pasquale
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy;
| | - Anna Moles
- Institute of Biomedical Research of Barcelona, Spanish Research Council, 08036 Barcelona, Spain;
| | - Luigi Michele Pavone
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy;
- Correspondence: ; Tel.: +39-081-7463043
| |
Collapse
|