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Shawky AM, Almalki FA, Alzahrani HA, Abdalla AN, Youssif BGM, Ibrahim NA, Gamal M, El-Sherief HAM, Abdel-Fattah MM, Hefny AA, Abdelazeem AH, Gouda AM. Covalent small-molecule inhibitors of SARS-CoV-2 Mpro: Insights into their design, classification, biological activity, and binding interactions. Eur J Med Chem 2024; 277:116704. [PMID: 39121741 DOI: 10.1016/j.ejmech.2024.116704] [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: 05/15/2024] [Revised: 07/10/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024]
Abstract
Since 2020, many compounds have been investigated for their potential use in the treatment of SARS-CoV-2 infection. Among these agents, a huge number of natural products and FDA-approved drugs have been evaluated as potential therapeutics for SARS-CoV-2 using virtual screening and docking studies. However, the identification of the molecular targets involved in viral replication led to the development of rationally designed anti-SARS-CoV-2 agents. Among these targets, the main protease (Mpro) is one of the key enzymes needed in the replication of the virus. The data gleaned from the crystal structures of SARS-CoV-2 Mpro complexes with small-molecule covalent inhibitors has been used in the design and discovery of many highly potent and broad-spectrum Mpro inhibitors. The current review focuses mainly on the covalent type of SARS-CoV-2 Mpro inhibitors. The design, chemistry, and classification of these inhibitors were also in focus. The biological activity of these inhibitors, including their inhibitory activities against Mpro, their antiviral activities, and the SAR studies, were discussed. The review also describes the potential mechanism of the interaction between these inhibitors and the catalytic Cys145 residue in Mpro. Moreover, the binding modes and key binding interactions of these covalent inhibitors were also illustrated. The covalent inhibitors discussed in this review were of diverse chemical nature and origin. Their antiviral activity was mediated mainly by the inhibition of SARS-CoV-2 Mpro, with IC50 values in the micromolar to the nanomolar range. Many of these inhibitors exhibited broad-spectrum inhibitory activity against the Mpro enzymes of other coronaviruses (SARS-CoV-1 and MERS-CoV). The dual inhibition of the Mpro and PLpro enzymes of SARS-CoV-2 could also provide higher therapeutic benefits than Mpro inhibition. Despite the approval of nirmatrelvir by the FDA, many mutations in the Mpro enzyme of SARS-CoV-2 have been reported. Although some of these mutations did not affect the potency of nirmatrelvir, there is an urgent need to develop a second generation of Mpro inhibitors. We hope that the data summarized in this review could help researchers in the design of a new potent generation of SARS-CoV-2 Mpro inhibitors.
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Affiliation(s)
- Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Faisal A Almalki
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Hayat Ali Alzahrani
- Applied Medical Science College, Medical Laboratory Technology Department, Northern Border University, Arar, Saudi Arabia
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia; Department of Pharmacology and Toxicology, Medicinal And Aromatic Plants Research Institute, National Center for Research, Khartoum, 2404, Sudan
| | - Bahaa G M Youssif
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut, 71526, Egypt.
| | - Nashwa A Ibrahim
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Mohammed Gamal
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Hany A M El-Sherief
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, Minia, Egypt
| | - Maha M Abdel-Fattah
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Ahmed A Hefny
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt; School of Pharmacy, University of Waterloo, Kitchener, Ontario, N2G 1C5, Canada
| | - Ahmed H Abdelazeem
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt; Pharmacy Department, College of Pharmacy, Nursing and Medical Sciences, Riyadh Elm University, Riyadh, 11681, Saudi Arabia
| | - Ahmed M Gouda
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt.
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2
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Ding S, Tian W, Lv Q, Miao Z, Xu L. A Nickel/Organoboron-Catalyzed Coupling of Aryl Bromides with Sodium Sulfinates: The Synthesis of Sulfones under Visible Light. Molecules 2024; 29:3418. [PMID: 39064996 PMCID: PMC11280069 DOI: 10.3390/molecules29143418] [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: 06/06/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
An efficient cross-coupling of aryl bromides with sodium sulfinates, using an organoboron photocatalyst with nickel, is described herein. Under the irradiation of white light, this dually catalytic system enables the synthesis of a series of sulfone compounds in moderate to good yields. A broad range of functional groups and heteroaromatic compounds is tolerated under these reaction conditions. The use of an organoboron photocatalyst highlights a sustainable alternative to iridium or ruthenium complexes. These findings contribute to the field of photochemistry and provide a greener approach to sulfone synthesis.
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Affiliation(s)
- Siyi Ding
- School of Electronic Information, Technological Institute of Materials & Energy Science (TIMES), Xi’an Key Laboratory of Advanced Photo-Electronics Materials and Energy Conversion Device, Xijing University, Xi’an 710123, China; (S.D.); (Q.L.)
| | - Weina Tian
- School of Chemistry and Chemical Engineering, State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, Shihezi University, Shihezi 832003, China;
| | - Qiaohuan Lv
- School of Electronic Information, Technological Institute of Materials & Energy Science (TIMES), Xi’an Key Laboratory of Advanced Photo-Electronics Materials and Energy Conversion Device, Xijing University, Xi’an 710123, China; (S.D.); (Q.L.)
| | - Zongcheng Miao
- School of Electronic Information, Technological Institute of Materials & Energy Science (TIMES), Xi’an Key Laboratory of Advanced Photo-Electronics Materials and Energy Conversion Device, Xijing University, Xi’an 710123, China; (S.D.); (Q.L.)
| | - Liang Xu
- School of Chemistry and Chemical Engineering, State Key Laboratory Incubation Base for Green Processing of Chemical Engineering, Shihezi University, Shihezi 832003, China;
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3
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Zimmer C, Brauer J, Ferenc D, Meyr J, Müller P, Räder HJ, Engels B, Opatz T, Schirmeister T. Substitution-Induced Mechanistic Switching in S NAr-Warheads for Cysteine Proteases. Molecules 2024; 29:2660. [PMID: 38893535 PMCID: PMC11173422 DOI: 10.3390/molecules29112660] [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: 04/25/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
The aim of this study was to investigate the transition from non-covalent reversible over covalent reversible to covalent irreversible inhibition of cysteine proteases by making delicate structural changes to the warhead scaffold. To this end, dipeptidic rhodesain inhibitors with different N-terminal electrophilic arenes as warheads relying on the SNAr mechanism were synthesized and investigated. Strong structure-activity relationships of the inhibition potency, the degree of covalency, and the reversibility of binding on the arene substitution pattern were found. The studies were complemented and substantiated by molecular docking and quantum-mechanical calculations of model systems. Furthermore, the improvement in the membrane permeability of peptide esters in comparison to their corresponding carboxylic acids was exemplified.
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Affiliation(s)
- Collin Zimmer
- Institute of Pharmaceutical and Biomedical Sciences, University of Mainz, Staudingerweg 5, 55128 Mainz, Germany; (C.Z.); (P.M.)
| | - Jan Brauer
- Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany; (J.B.); (D.F.)
| | - Dorota Ferenc
- Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany; (J.B.); (D.F.)
| | - Jessica Meyr
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany; (J.M.); (B.E.)
| | - Patrick Müller
- Institute of Pharmaceutical and Biomedical Sciences, University of Mainz, Staudingerweg 5, 55128 Mainz, Germany; (C.Z.); (P.M.)
| | - Hans-Joachim Räder
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany;
| | - Bernd Engels
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany; (J.M.); (B.E.)
| | - Till Opatz
- Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany; (J.B.); (D.F.)
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, University of Mainz, Staudingerweg 5, 55128 Mainz, Germany; (C.Z.); (P.M.)
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4
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Pi S, Xiong S, Yuan Y, Deng H. The Role of Inflammasome in Abdominal Aortic Aneurysm and Its Potential Drugs. Int J Mol Sci 2024; 25:5001. [PMID: 38732221 PMCID: PMC11084561 DOI: 10.3390/ijms25095001] [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: 04/07/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024] Open
Abstract
Abdominal aortic aneurysm (AAA) has been recognized as a serious chronic inflammatory degenerative aortic disease in recent years. At present, there is no other effective intervention except surgical treatment for AAA. With the aging of the human population, its incidence is increasing year by year, posing a serious threat to human health. Modern studies suggest that vascular chronic inflammatory response is the core process in AAA occurrence and development. Inflammasome, a multiprotein complex located in the cytoplasm, mediates the expression of various inflammatory cytokines like interleukin (IL)-1β and IL-18, and thus plays a pivotal role in inflammation regulation. Therefore, inflammasome may exert a crucial influence on the progression of AAA. This article reviews some mechanism studies to investigate the role of inflammasome in AAA and then summarizes several potential drugs targeting inflammasome for the treatment of AAA, aiming to provide new ideas for the clinical prevention and treatment of AAA beyond surgical methods.
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Affiliation(s)
- Suyu Pi
- Department of Vascular Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China; (S.P.); (S.X.); (Y.Y.)
- Aortic Abdominal Aneurysm (AAA) Translational Medicine Research Center of Hubei Province, Wuhan 430060, China
| | - Sizheng Xiong
- Department of Vascular Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China; (S.P.); (S.X.); (Y.Y.)
- Aortic Abdominal Aneurysm (AAA) Translational Medicine Research Center of Hubei Province, Wuhan 430060, China
| | - Yan Yuan
- Department of Vascular Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China; (S.P.); (S.X.); (Y.Y.)
- Aortic Abdominal Aneurysm (AAA) Translational Medicine Research Center of Hubei Province, Wuhan 430060, China
| | - Hongping Deng
- Department of Vascular Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China; (S.P.); (S.X.); (Y.Y.)
- Aortic Abdominal Aneurysm (AAA) Translational Medicine Research Center of Hubei Province, Wuhan 430060, China
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Reddy RJ, Kumar JJ, Kumari AH. Recent trends in the synthesis and applications of β-iodovinyl sulfones: a decade of progress. Org Biomol Chem 2024; 22:2492-2509. [PMID: 38446020 DOI: 10.1039/d3ob01980b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Direct vicinal difunctionalization of π-systems has emerged as a powerful platform for constructing multiple bonds in a single synthetic operation using simple chemical feedstocks. Over the past decade, there has been exponential growth in the direct construction of successive C-S and C-I bonds using a wide variety of sulfonyl and iodide reactants through 1,2-iodosulfonylation of alkynes in a regio- and stereo-selective manner. In this review, we mainly focus on the recent developments in the preparation of β-iodovinyl sulfones and their practical applications in organic synthesis. The most promising photoredox and electrochemical transformations for synthesizing β-iodovinyl sulfones are also reviewed. The multifunctional β-iodovinyl sulfones have recently been burgeoning as versatile synthetic precursors due to the combination of vinyl iodide and vinyl sulfone moieties, essential building blocks for diverse synthetic manipulations. We hereby present the chemistry of β-iodovinyl sulfones, which can be classified into numerous sections based on the sulfonyl surrogates, and potential synthetic approaches are systematically outlined.
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Affiliation(s)
- Raju Jannapu Reddy
- Department of Chemistry, University College of Science, Osmania University, Hyderabad 500 007, India.
| | - Jangam Jagadesh Kumar
- Department of Chemistry, University College of Science, Osmania University, Hyderabad 500 007, India.
| | - Arram Haritha Kumari
- Department of Chemistry, University College of Science, Osmania University, Hyderabad 500 007, India.
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6
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Anderton AS, Knowles OJ, Rossi-Ashton JA, Procter DJ. Flavin-Mediated Photocatalysis Provides a General Platform for Sulfide C-H Functionalization. ACS Catal 2024; 14:2395-2401. [PMID: 38384945 PMCID: PMC10877610 DOI: 10.1021/acscatal.3c05785] [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: 11/28/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/23/2024]
Abstract
Functionalized sulfides are important in many areas of science, ranging from chemical biology through drug discovery to organic materials chemistry. Sulfides bearing pendant reactive groups in the α-position are particularly useful; however, methods for the selective valorization of simple sulfides or the late-stage functionalization of complex sulfides by the convenient addition of valuable functionality are underexplored. Here we exemplify a general reaction platform for sulfide functionalization by showcasing three modes of α-sulfur C-H functionalization; cyanation, alkenylation, and alkynylation. Using inexpensive and commercially available riboflavin tetraacetate and visible light, decoration of both feedstock and complex sulfides proceeds in a good yield and with high selectivity. Methionine-containing peptides can also be selectively functionalized and a tolerance screen using amino-acid dopants suggests that the platform is compatible with most amino-acid side chains and thus is a potential tool for bioconjugation.
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Affiliation(s)
| | | | - James A. Rossi-Ashton
- Department of Chemistry, University
of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - David J. Procter
- Department of Chemistry, University
of Manchester, Oxford Road, Manchester M13 9PL, U.K.
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7
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Giroud M, Kuhn B, Haap W. Drug Discovery Efforts to Identify Novel Treatments for Neglected Tropical Diseases - Cysteine Protease Inhibitors. Curr Med Chem 2024; 31:2170-2194. [PMID: 37916489 DOI: 10.2174/0109298673249097231017051733] [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: 02/14/2023] [Revised: 06/19/2023] [Accepted: 09/14/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Neglected tropical diseases are a severe burden for mankind, affecting an increasing number of people around the globe. Many of those diseases are caused by protozoan parasites in which cysteine proteases play a key role in the parasite's pathogenesis. OBJECTIVE In this review article, we summarize the drug discovery efforts of the research community from 2017 - 2022 with a special focus on the optimization of small molecule cysteine protease inhibitors in terms of selectivity profiles or drug-like properties as well as in vivo studies. The cysteine proteases evaluated by this methodology include Cathepsin B1 from Schistosoma mansoni, papain, cruzain, falcipain, and rhodesain. METHODS Exhaustive literature searches were performed using the keywords "Cysteine Proteases" and "Neglected Tropical Diseases" including the years 2017 - 2022. Overall, approximately 3'000 scientific papers were retrieved, which were filtered using specific keywords enabling the focus on drug discovery efforts. RESULTS AND CONCLUSION Potent and selective cysteine protease inhibitors to treat neglected tropical diseases were identified, which progressed to pharmacokinetic and in vivo efficacy studies. As far as the authors are aware of, none of those inhibitors reached the stage of active clinical development. Either the inhibitor's potency or pharmacokinetic properties or safety profile or a combination thereof prevented further development of the compounds. More efforts with particular emphasis on optimizing pharmacokinetic and safety properties are needed, potentially by collaborations of academic and industrial research groups with complementary expertise. Furthermore, new warheads reacting with the catalytic cysteine should be exploited to advance the research field in order to make a meaningful impact on society.
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Affiliation(s)
- Maude Giroud
- Pharma Research and Early Development pRED, Roche Innovation Center Basel, Medicinal Chemistry, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, Basel, CH-4070, Switzerland
| | - Bernd Kuhn
- Pharma Research and Early Development pRED, Roche Innovation Center Basel, Medicinal Chemistry, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, Basel, CH-4070, Switzerland
| | - Wolfgang Haap
- Pharma Research and Early Development pRED, Roche Innovation Center Basel, Medicinal Chemistry, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, Basel, CH-4070, Switzerland
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8
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González JEH, Salas-Sarduy E, Alvarez LH, Valiente PA, Arni RK, Pascutti PG. Three Decades of Targeting Falcipains to Develop Antiplasmodial Agents: What have we Learned and What can be Done Next? Curr Med Chem 2024; 31:2234-2263. [PMID: 37711130 DOI: 10.2174/0929867331666230913165219] [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: 03/28/2023] [Revised: 05/06/2023] [Accepted: 07/25/2023] [Indexed: 09/16/2023]
Abstract
Malaria is a devastating infectious disease that affects large swathes of human populations across the planet's tropical regions. It is caused by parasites of the genus Plasmodium, with Plasmodium falciparum being responsible for the most lethal form of the disease. During the intraerythrocytic stage in the human hosts, malaria parasites multiply and degrade hemoglobin (Hb) using a battery of proteases, which include two cysteine proteases, falcipains 2 and 3 (FP-2 and FP-3). Due to their role as major hemoglobinases, FP-2 and FP-3 have been targeted in studies aiming to discover new antimalarials and numerous inhibitors with activity against these enzymes, and parasites in culture have been identified. Nonetheless, cross-inhibition of human cysteine cathepsins remains a serious hurdle to overcome for these compounds to be used clinically. In this article, we have reviewed key functional and structural properties of FP-2/3 and described different compound series reported as inhibitors of these proteases during decades of active research in the field. Special attention is also paid to the wide range of computer-aided drug design (CADD) techniques successfully applied to discover new active compounds. Finally, we provide guidelines that, in our understanding, will help advance the rational discovery of new FP-2/3 inhibitors.
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Affiliation(s)
- Jorge Enrique Hernández González
- Multiuser Center for Biomolecular Innovation, IBILCE/UNESP, São José do Rio Preto, SP, Brazil
- Department of Pharmaceutical Sciences, UZA II, University of Vienna, Vienna, 1090, Austria
| | - Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo Ugalde, Universidad Nacional de San Martín, CONICET, San Martín, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnología (EByN), Universidad de San Martín (UNSAM), San Martín, Buenos Aires, Argentina
| | | | - Pedro Alberto Valiente
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada
| | | | - Pedro Geraldo Pascutti
- Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, RJ, Brazil
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Alves ETM, Pernichelle FG, Nascimento LA, Ferreira GM, Ferreira EI. Covalent Inhibitors for Neglected Diseases: An Exploration of Novel Therapeutic Options. Pharmaceuticals (Basel) 2023; 16:1028. [PMID: 37513939 PMCID: PMC10385647 DOI: 10.3390/ph16071028] [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: 03/24/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Neglected diseases, primarily found in tropical regions of the world, present a significant challenge for impoverished populations. Currently, there are 20 diseases considered neglected, which greatly impact the health of affected populations and result in difficult-to-control social and economic consequences. Unfortunately, for the majority of these diseases, there are few or no drugs available for patient treatment, and the few drugs that do exist often lack adequate safety and efficacy. As a result, there is a pressing need to discover and design new drugs to address these neglected diseases. This requires the identification of different targets and interactions to be studied. In recent years, there has been a growing focus on studying enzyme covalent inhibitors as a potential treatment for neglected diseases. In this review, we will explore examples of how these inhibitors have been used to target Human African Trypanosomiasis, Chagas disease, and Malaria, highlighting some of the most promising results so far. Ultimately, this review aims to inspire medicinal chemists to pursue the development of new drug candidates for these neglected diseases, and to encourage greater investment in research in this area.
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Affiliation(s)
- Erick Tavares Marcelino Alves
- Department of Pharmacy, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
| | - Filipe Gomes Pernichelle
- Department of Pharmacy, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
| | - Lucas Adriano Nascimento
- Department of Pharmacy, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
| | - Elizabeth Igne Ferreira
- Department of Pharmacy, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
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10
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Fonte M, Fontinha D, Moita D, Caño-Prades O, Avalos-Padilla Y, Fernàndez-Busquets X, Prudêncio M, Gomes P, Teixeira C. New 4-(N-cinnamoylbutyl)aminoacridines as potential multi-stage antiplasmodial leads. Eur J Med Chem 2023; 258:115575. [PMID: 37390511 DOI: 10.1016/j.ejmech.2023.115575] [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: 04/14/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 07/02/2023]
Abstract
A novel family of 4-aminoacridine derivatives was obtained by linking this heteroaromatic core to different trans-cinnamic acids. The 4-(N-cinnamoylbutyl)aminoacridines obtained exhibited in vitro activity in the low- or sub-micromolar range against (i) hepatic stages of Plasmodium berghei, (ii) erythrocytic forms of Plasmodium falciparum, and (iii) early and mature gametocytes of Plasmodium falciparum. The most active compound, having a meta-fluorocinnamoyl group linked to the acridine core, was 20- and 120-fold more potent, respectively, against the hepatic and gametocyte stages of Plasmodium infection than the reference drug, primaquine. Moreover, no cytotoxicity towards mammalian and red blood cells at the concentrations tested was observed for any of the compounds under investigation. These novel conjugates represent promising leads for the development of new multi-target antiplasmodials.
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Affiliation(s)
- Mélanie Fonte
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Portugal.
| | - Diana Fontinha
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Diana Moita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Omar Caño-Prades
- Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Yunuen Avalos-Padilla
- Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Xavier Fernàndez-Busquets
- Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain; Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-Universitat de Barcelona), Spain; Nanoscience and Nanotechnology Institute (IN2UB), University of Barcelona, Spain
| | - Miguel Prudêncio
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Paula Gomes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Portugal.
| | - Cátia Teixeira
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Portugal; Gyros Protein Technologies Inc., Tucson, AZ, USA
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11
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Santos VC, Leite PG, Santos LH, Pascutti PG, Kolb P, Machado FS, Ferreira RS. Structure-based discovery of novel cruzain inhibitors with distinct trypanocidal activity profiles. Eur J Med Chem 2023; 257:115498. [PMID: 37290182 DOI: 10.1016/j.ejmech.2023.115498] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 06/10/2023]
Abstract
Over 110 years after the first formal description of Chagas disease, the trypanocidal drugs thus far available have limited efficacy and several side effects. This encourages the search for novel treatments that inhibit T. cruzi targets. One of the most studied anti-T. cruzi targets is the cysteine protease cruzain; it is associated with metacyclogenesis, replication, and invasion of the host cells. We used computational techniques to identify novel molecular scaffolds that act as cruzain inhibitors. First, with a docking-based virtual screening, we identified compound 8, a competitive cruzain inhibitor with a Ki of 4.6 μM. Then, aided by molecular dynamics simulations, cheminformatics, and docking, we identified the analog compound 22 with a Ki of 27 μM. Surprisingly, despite sharing the same isoquinoline scaffold, compound 8 presented higher trypanocidal activity against the epimastigote forms, while compound 22, against the trypomastigotes and amastigotes. Taken together, compounds 8 and 22 represent a promising scaffold for further development of trypanocidal compounds as drug candidates for treating Chagas disease.
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Affiliation(s)
- Viviane Corrêa Santos
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Paulo Gaio Leite
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Lucianna Helene Santos
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Pedro Geraldo Pascutti
- Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Rio de Janeiro, RJ, CEP 21944-970, Brazil
| | - Peter Kolb
- Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35037, Marburg, Germany
| | - Fabiana Simão Machado
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Rafaela Salgado Ferreira
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil.
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12
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Arafet K, Royo S, Schirmeister T, Barthels F, González FV, Moliner V. Impact of the Recognition Part of Dipeptidyl Nitroalkene Compounds on the Inhibition Mechanism of Cysteine Proteases Cruzain and Cathepsin L. ACS Catal 2023; 13:6289-6300. [PMID: 37180968 PMCID: PMC10167892 DOI: 10.1021/acscatal.3c01035] [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: 03/06/2023] [Revised: 04/10/2023] [Indexed: 05/16/2023]
Abstract
Cysteine proteases (CPs) are an important class of enzymes, many of which are responsible for several human diseases. For instance, cruzain of protozoan parasite Trypanosoma cruzi is responsible for the Chagas disease, while the role of human cathepsin L is associated with some cancers or is a potential target for the treatment of COVID-19. However, despite paramount work carried out during the past years, the compounds that have been proposed so far show limited inhibitory action against these enzymes. We present a study of proposed covalent inhibitors of these two CPs, cruzain and cathepsin L, based on the design, synthesis, kinetic measurements, and QM/MM computational simulations on dipeptidyl nitroalkene compounds. The experimentally determined inhibition data, together with the analysis and the predicted inhibition constants derived from the free energy landscape of the full inhibition process, allowed describing the impact of the recognition part of these compounds and, in particular, the modifications on the P2 site. The designed compounds and, in particular, the one with a bulky group (Trp) at the P2 site show promising in vitro inhibition activities against cruzain and cathepsin L for use as a starting lead compound in the development of drugs with medical applications for the treatment of human diseases and future designs.
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Affiliation(s)
- Kemel Arafet
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, 43124 Parma, Italy
- BioComp
Group, Institute of Advanced Materials (INAM),
Universitat Jaume I, 12071 Castelló, Spain
| | - Santiago Royo
- Departament
de Química Inorgànica i Orgànica, Universitat Jaume I, 12071 Castelló, Spain
| | - Tanja Schirmeister
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | - Fabian Barthels
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | - Florenci V. González
- Departament
de Química Inorgànica i Orgànica, Universitat Jaume I, 12071 Castelló, Spain
| | - Vicent Moliner
- BioComp
Group, Institute of Advanced Materials (INAM),
Universitat Jaume I, 12071 Castelló, Spain
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13
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Previti S, Ettari R, Di Chio C, Legac J, Bogacz M, Zimmer C, Schirmeister T, Rosenthal PJ, Zappalà M. Influence of amino acid size at the P3 position of N-Cbz-tripeptide Michael acceptors targeting falcipain-2 and rhodesain for the treatment of malaria and human african trypanosomiasis. Bioorg Chem 2023; 137:106587. [PMID: 37163812 DOI: 10.1016/j.bioorg.2023.106587] [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: 01/20/2023] [Revised: 04/18/2023] [Accepted: 05/01/2023] [Indexed: 05/12/2023]
Abstract
In recent decades, several structure-activity relationship (SAR) studies provided potent inhibitors of the cysteine proteases falcipain-2 (FP-2) and rhodesain (RD) from Plasmodium falciparum and Trypanosoma brucei rhodesiense, respectively. Whilst the roles of the warhead and residues targeting the P1 and P2 pockets of the proteases were extensively investigated, the roles of the amino acids occupying the S3 pocket were not widely assessed. Herein we report the synthesis and biological evaluation of a set of novel Michael acceptors bearing amino acids of increasing size at the P3 site (1a-g/2a-g, SPR20-SPR33) against FP-2, RD, P. falciparum, and T. brucei. Overall, the Michael acceptors bearing small amino acids at the P3 site exhibited the most potent inhibitory properties towards FP-2. In contrast, analogues with bulky residues at the P3 position were very potent rhodesain inhibitors. In cell based assays, single-digit micromolar EC50 values against the two protozoa were observed. These findings can be a starting point for the development of peptide-based FP-2 and RD inhibitors.
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Affiliation(s)
- Santo Previti
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale Stagno d'Alcontres 31, 98166 Messina, Italy.
| | - Roberta Ettari
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Carla Di Chio
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Jenny Legac
- Department of Medicine, University of California, San Francisco, CA 94143, United States
| | - Marta Bogacz
- Institute of Organic Chemistry & Macromolecular Chemistry, Friedrich-Schiller-University of Jena, 07743 Jena, Germany
| | - Collin Zimmer
- Institute of Pharmaceutical and Biomedical Sciences, University of Mainz, 55128 Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, University of Mainz, 55128 Mainz, Germany
| | - Philip J Rosenthal
- Department of Medicine, University of California, San Francisco, CA 94143, United States
| | - Maria Zappalà
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale Stagno d'Alcontres 31, 98166 Messina, Italy
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14
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Müller P, Meta M, Meidner JL, Schwickert M, Meyr J, Schwickert K, Kersten C, Zimmer C, Hammerschmidt SJ, Frey A, Lahu A, de la Hoz-Rodríguez S, Agost-Beltrán L, Rodríguez S, Diemer K, Neumann W, Gonzàlez FV, Engels B, Schirmeister T. Investigation of the Compatibility between Warheads and Peptidomimetic Sequences of Protease Inhibitors-A Comprehensive Reactivity and Selectivity Study. Int J Mol Sci 2023; 24:ijms24087226. [PMID: 37108388 PMCID: PMC10138721 DOI: 10.3390/ijms24087226] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Covalent peptidomimetic protease inhibitors have gained a lot of attention in drug development in recent years. They are designed to covalently bind the catalytically active amino acids through electrophilic groups called warheads. Covalent inhibition has an advantage in terms of pharmacodynamic properties but can also bear toxicity risks due to non-selective off-target protein binding. Therefore, the right combination of a reactive warhead with a well-suited peptidomimetic sequence is of great importance. Herein, the selectivities of well-known warheads combined with peptidomimetic sequences suited for five different proteases were investigated, highlighting the impact of both structure parts (warhead and peptidomimetic sequence) for affinity and selectivity. Molecular docking gave insights into the predicted binding modes of the inhibitors inside the binding pockets of the different enzymes. Moreover, the warheads were investigated by NMR and LC-MS reactivity assays against serine/threonine and cysteine nucleophile models, as well as by quantum mechanics simulations.
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Affiliation(s)
- Patrick Müller
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Mergim Meta
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Jan Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Jessica Meyr
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Kevin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Collin Zimmer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Stefan Josef Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Ariane Frey
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Albin Lahu
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | | | - Laura Agost-Beltrán
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló de la Pana, Spain
| | - Santiago Rodríguez
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló de la Pana, Spain
| | - Kira Diemer
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Wilhelm Neumann
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Florenci V Gonzàlez
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló de la Pana, Spain
| | - Bernd Engels
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
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15
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Sheir SK, Elmongy EI, Mohamad AH, Osman GY, Bendary SE, Ahmed AAS, Binsuwaidan R, El-Sayed IET. Molluscicidal and Larvicidal Potency of N-Heterocylic Analogs against Biomophalaria alexandrina Snails and Schistosoma mansoni Larval Stages. Pharmaceutics 2023; 15:pharmaceutics15041200. [PMID: 37111685 PMCID: PMC10142358 DOI: 10.3390/pharmaceutics15041200] [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: 02/16/2023] [Revised: 03/22/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
This work describes the synthesis of quinoline-based N--heterocyclic arenes and their biological evaluation as molluscicides against adult Biomophalaria alexandrina snails as well as larvicides against Schistosoma mansoni larvae (miracidia and cercariae). Molecular docking studies were demonstrated to investigate their affinity for cysteine protease protein as an interesting target for antiparasitics. Compound AEAN showed the best docking results followed by APAN in comparison to the co-crystallized ligand D1R reflected by their binding affinities and RMSD values. The egg production, hatchability of B. alexandrina snails and ultrastructural topography of S. mansoni cercariae using SEM were assessed. Biological evaluations (hatchability and egg-laying capacity) revealed that the quinoline hydrochloride salt CAAQ was the most effective compound against adult B. alexandrina snails, whereas the indolo-quinoline derivative APAN had the most efficiency against miracidia, and the acridinyl derivative AEAA was the most effective against cercariae and caused 100% mortality. CAAQ and AEAA were found to modulate the biological responses of B. alexandrina snails with/without S. mansoni infection and larval stages that will affect S. mansoni infection. AEAA caused deleterious morphological effects on cercariae. CAAQ caused inhibition in the number of eggs/snail/week and reduced reproductive rate to 43.8% in all the experimental groups. CAAQ and AEAA can be recommended as an effective molluscicide of plant origin for the control program of schistosomiasis.
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Affiliation(s)
- Sherin K Sheir
- Zoology Department, Faculty of Science, Menoufia University, Shibin El Kom 32511, Egypt
| | - Elshaymaa I Elmongy
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Azza H Mohamad
- Zoology Department, Faculty of Science, Menoufia University, Shibin El Kom 32511, Egypt
| | - Gamalat Y Osman
- Zoology Department, Faculty of Science, Menoufia University, Shibin El Kom 32511, Egypt
| | - Shimaa E Bendary
- Zoology Department, Faculty of Science, Menoufia University, Shibin El Kom 32511, Egypt
| | - Abdullah A S Ahmed
- Chemistry Department, Faculty of Science, Menoufia University, Shibin El-Kom 32511, Egypt
| | - Reem Binsuwaidan
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
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16
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Jasinski G, Salas-Sarduy E, Vega D, Fabian L, Florencia Martini M, Moglioni AG. Design, synthesis and biological evaluation of novel thiosemicarbazones as cruzipain inhibitors. Eur J Med Chem 2023; 254:115345. [PMID: 37054562 DOI: 10.1016/j.ejmech.2023.115345] [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: 01/30/2023] [Revised: 03/23/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
Based on the activity of 23 TSCs on CZ taken from the literature, we have developed a QSAR model for predicting the activity of TSCs. New TSCs were designed and then tested against CZP, resulting in inhibitors with IC50 values in the nanomolar range. The modelling of the corresponding TSC-CZ complexes by molecular docking and QM/QM ONIOM refinement indicates a binding mode compatible with what was expected for active TSCs, according to a geometry-based theoretical model previously developed by our research group. Kinetic experiments on CZP suggest that the new TSCs act by a mechanism that involves the formation of a reversible covalent adduct with slow association and dissociation kinetics. These results demonstrate the strong inhibitory effect of the new TSCs and the benefit of the combined use of QSAR and molecular modelling techniques in the design of new and potent CZ/CZP inhibitors.
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Affiliation(s)
- Gabriel Jasinski
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Química Medicinal, Buenos Aires, C1113AAD, Argentina; CONICET-Universidad de Buenos Aires, Instituto de la Química y el Metabolismo del Fármaco (IQUIMEFA), Buenos Aires, 1113, Argentina
| | - Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo Ugalde" (IIBIO), CONICET, San Martín, Buenos Aires, 1650, Argentina; Escuela de Bio y Nanotecnología (EByN), Universidad Nacional de San Martín (UNSAM), San Martín, Buenos Aires, 1650, Argentina
| | - Daniel Vega
- Departamento de Física de la Materia Condensada, GIyA, CAC, CNEA, Buenos Aires, B1650KNA, Argentina; Escuela de Ciencia y Tecnología, UNSAM, San Martín, Buenos Aires, B1650KNA, Argentina
| | - Lucas Fabian
- CONICET-Universidad de Buenos Aires, Instituto de la Química y el Metabolismo del Fármaco (IQUIMEFA), Buenos Aires, 1113, Argentina
| | - M Florencia Martini
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Química Medicinal, Buenos Aires, C1113AAD, Argentina; CONICET-Universidad de Buenos Aires, Instituto de la Química y el Metabolismo del Fármaco (IQUIMEFA), Buenos Aires, 1113, Argentina
| | - Albertina G Moglioni
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Cátedra de Química Medicinal, Buenos Aires, C1113AAD, Argentina; CONICET-Universidad de Buenos Aires, Instituto de la Química y el Metabolismo del Fármaco (IQUIMEFA), Buenos Aires, 1113, Argentina.
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17
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Patra J, Rana D, Arora S, Pal M, Mahindroo N. Falcipains: Biochemistry, target validation and structure-activity relationship studies of inhibitors as antimalarials. Eur J Med Chem 2023; 252:115299. [PMID: 36996716 DOI: 10.1016/j.ejmech.2023.115299] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/04/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023]
Abstract
Malaria is a tropical disease with significant morbidity and mortality burden caused by Plasmodium species in Africa, the Middle East, Asia, and South America. Pathogenic Plasmodium species have lately become increasingly resistant to approved chemotherapeutics and combination therapies. Therefore, there is an emergent need for identifying new druggable targets and novel chemical classes against the parasite. Falcipains, cysteine proteases required for heme metabolism in the erythrocytic stage, have emerged as promising drug targets against Plasmodium species that infect humans. This perspective discusses the biology, biochemistry, structural features, and genetics of falcipains. The efforts to identify selective or dual inhibitors and their structure-activity relationships are reviewed to give a perspective on the design of novel compounds targeting falcipains for antimalarial activity evaluating reasons for hits and misses for this important target.
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Affiliation(s)
- Jeevan Patra
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Energy Acres, Bidholi, Via Prem Nagar, Uttarakhand, 248007, India
| | - Devika Rana
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh, 173229, India
| | - Smriti Arora
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Energy Acres, Bidholi, Via Prem Nagar, Uttarakhand, 248007, India
| | - Mintu Pal
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Bathinda, Punjab, 151001, India
| | - Neeraj Mahindroo
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Energy Acres, Bidholi, Via Prem Nagar, Uttarakhand, 248007, India; School of Health Sciences and Technology, Dr. Vishwanath Karad MIT World Peace University, 124 Paud Road, Kothrud, Pune, Maharashtra, 411038, India.
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18
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Melfi F, Carradori S, Campestre C, Haloci E, Ammazzalorso A, Grande R, D'Agostino I. Emerging compounds and therapeutic strategies to treat infections from Trypanosoma brucei: an overhaul of the last 5-years patents. Expert Opin Ther Pat 2023; 33:247-263. [PMID: 36933190 DOI: 10.1080/13543776.2023.2193328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
INTRODUCTION Human African Trypanosomiasis is a neglected disease caused by infection from parasites belonging to the Trypanosoma brucei species. Only six drugs are currently available and employed depending on the stage of the infection: pentamidine, suramin, melarsoprol, eflornithine, nifurtimox, and fexinidazole. Joint research projects were launched in an attempt to find new therapeutic options for this severe and often lethal disease. AREAS COVERED After a brief description of the recent literature on the parasite and the disease, we searched for patents dealing with the proposal of new anti-trypanosomiasis agents and, following the PRISMA guidelines, we filtered the results to those published from 2018onwards returning suitable entries, which represent the contemporary landscape of compounds/strategies against Trypanosoma brucei. In addition, some relevant publications from the overall scientific literature were also discussed. EXPERT OPINION This review comprehensively covers and analyzes the most recent advances not only in the discovery of new inhibitors and their structure-activity relationships but also in the assessment of innovative biological targets opening new scenarios in the MedChem field. Lastly, also new vaccines and formulations recently patented were described. However, natural and synthetic compounds were analyzed in terms of inhibitory activity and selective toxicity against human cells.
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Affiliation(s)
- Francesco Melfi
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Simone Carradori
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Cristina Campestre
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Entela Haloci
- Department of Pharmacy, University of Medicine, Tirana, Albania
| | | | - Rossella Grande
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Ilaria D'Agostino
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
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Screening the Pathogen Box to Discover and Characterize New Cruzain and TbrCatL Inhibitors. Pathogens 2023; 12:pathogens12020251. [PMID: 36839523 PMCID: PMC9967275 DOI: 10.3390/pathogens12020251] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Chagas disease and Human African Trypanosomiasis, caused by Trypanosoma cruzi and T. brucei, respectively, pose relevant health challenges throughout the world, placing 65 to 70 million people at risk each. Given the limited efficacy and severe side effects associated with current chemotherapy, new drugs are urgently needed for both diseases. Here, we report the screening of the Pathogen Box collection against cruzain and TbrCatL, validated targets for Chagas disease and Human African Trypanosomiasis, respectively. Enzymatic assays were applied to screen 400 compounds, validate hits, determine IC50 values and, when possible, mechanisms of inhibition. In this case, 12 initial hits were obtained and ten were prioritized for follow-up. IC50 values were obtained for six of them (hit rate = 1.5%) and ranged from 0.46 ± 0.03 to 27 ± 3 µM. MMV687246 was found to be a mixed inhibitor of cruzain (Ki = 57 ± 6 µM) while MMV688179 was found to be a competitive inhibitor of cruzain with a nanomolar potency (Ki = 165 ± 63 nM). A putative binding mode for MMV688179 was obtained by docking. The six hits discovered against cruzain and TbrCatL are of great interest for further optimization by the medicinal chemistry community.
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20
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Flavonoid Derivatives as New Potent Inhibitors of Cysteine Proteases: An Important Step toward the Design of New Compounds for the Treatment of Leishmaniasis. Microorganisms 2023; 11:microorganisms11010225. [PMID: 36677517 PMCID: PMC9866541 DOI: 10.3390/microorganisms11010225] [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: 11/16/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Leishmaniasis is a neglected tropical disease, affecting more than 350 million people globally. However, there is currently no vaccine available against human leishmaniasis, and current treatment is hampered by high cost, side-effects, and painful administration routes. It has become a United Nations goal to end leishmaniasis epidemics by 2030, and multitarget drug strategy emerges as a promising alternative. Among the multitarget compounds, flavonoids are a renowned class of natural products, and a structurally diverse library can be prepared through organic synthesis, which can be tested for biological effectiveness. In this study, we synthesised 17 flavonoid analogues using a scalable, easy-to-reproduce, and inexpensive method. All synthesised compounds presented an impressive inhibition capacity against rCPB2.8, rCPB3, and rH84Y enzymes, which are highly expressed in the amastigote stage, the target form of the parasite. Compounds 3c, f12a, and f12b were found to be effective against all isoforms. Furthermore, their intermolecular interactions were also investigated through a molecular modelling study. These compounds were highly potent against the parasite and demonstrated low cytotoxic action against mammalian cells. These results are pioneering, representing an advance in the investigation of the mechanisms behind the antileishmanial action of flavonoid derivatives. Moreover, compounds have been shown to be promising leads for the design of other cysteine protease inhibitors for the treatment of leishmaniasis diseases.
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21
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Role of NLRP3 Inflammasome and Its Inhibitors as Emerging Therapeutic Drug Candidate for Alzheimer's Disease: a Review of Mechanism of Activation, Regulation, and Inhibition. Inflammation 2023; 46:56-87. [PMID: 36006570 PMCID: PMC9403980 DOI: 10.1007/s10753-022-01730-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/26/2022] [Indexed: 02/06/2023]
Abstract
Alzheimer's disease (AD) is one of the most prevalent neurodegenerative disorders. The etiology and pathology of AD are complicated, variable, and yet to be completely discovered. However, the involvement of inflammasomes, particularly the NLRP3 inflammasome, has been emphasized recently. NLRP3 is a critical pattern recognition receptor involved in the expression of immune responses and has been found to play a significant role in the development of various immunological and neurological disorders such as multiple sclerosis, ulcerative colitis, gout, diabetes, and AD. It is a multimeric protein which releases various cytokines and causes caspase-1 activation through the process known as pyroptosis. Increased levels of cytokines (IL-1β and IL-18), caspase-1 activation, and neuropathogenic stimulus lead to the formation of proinflammatory microglial M1. Progressive researches have also shown that besides loss of neurons, the pathophysiology of AD primarily includes amyloid beta (Aβ) accumulation, generation of oxidative stress, and microglial damage leading to activation of NLRP3 inflammasome that eventually leads to neuroinflammation and dementia. It has been suggested in the literature that suppressing the activity of the NLRP3 inflammasome has substantial potential to prevent, manage, and treat Alzheimer's disease. The present review discusses the functional composition, various models, signaling molecules, pathways, and evidence of NLRP3 activation in AD. The manuscript also discusses the synthetic drugs, their clinical status, and projected natural products as a potential therapeutic approach to manage and treat NLRP3 mediated AD.
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22
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Danazumi AU, Balogun EO. Microsecond-long simulation reveals the molecular mechanism for the dual inhibition of falcipain-2 and falcipain-3 by antimalarial lead compounds. Front Mol Biosci 2022; 9:1070080. [PMID: 36601587 PMCID: PMC9806354 DOI: 10.3389/fmolb.2022.1070080] [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: 10/14/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
The latest world malaria report revealed that human deaths caused by malaria are currently on the rise and presently stood at over 627,000 per year. In addition, more than 240 million people have the infection at any given time. These figures make malaria the topmost infectious disease and reiterate the need for continuous efforts for the development of novel chemotherapies. Malaria is an infectious disease caused majorly by the protozoan intracellular parasite Plasmodium falciparum and transmitted by mosquitoes. Reports abound on the central role of falcipains (cysteine protease enzymes) in the catabolism of hemoglobin for furnishing the plasmodium cells with amino acids that they require for development and survival in the hosts. Even though falcipains (FPs) have been validated as drug target molecules for the development of new antimalarial drugs, none of its inhibitory compounds have advanced beyond the early discovery stage. Therefore, there are renewed efforts to expand the collection of falcipain inhibitors. As a result, an interesting finding reported the discovery of a quinolinyl oxamide derivative (QOD) and an indole carboxamide derivative (ICD), with each compound demonstrating good potencies against the two essential FP subtypes 2 (FP-2) and 3 (FP-3). In this study, we utilized microsecond-scale molecular dynamics simulation computational method to investigate the interactions between FP-2 and FP-3 with the quinolinyl oxamide derivative and indole carboxamide derivative. The results revealed that quinolinyl oxamide derivative and indole carboxamide derivative bound tightly at the active site of both enzymes. Interestingly, despite belonging to different chemical scaffolds, they are coordinated by almost identical amino acid residues via extensive hydrogen bond interactions in both FP-2 and FP-3. Our report provided molecular insights into the interactions between FP-2 and FP-3 with quinolinyl oxamide derivative and indole carboxamide derivative, which we hope will pave the way towards the design of more potent and druglike inhibitors of these enzymes and will pave the way for their development to new antimalarial drugs.
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Affiliation(s)
- Ammar Usman Danazumi
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland,Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Emmanuel Oluwadare Balogun
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria,Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria,Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, San Diego, CA, United States,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,*Correspondence: Emmanuel Oluwadare Balogun, ,
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23
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Lemke C, Jílková A, Ferber D, Braune A, On A, Johe P, Zíková A, Schirmeister T, Mareš M, Horn M, Gütschow M. Two Tags in One Probe: Combining Fluorescence- and Biotin-based Detection of the Trypanosomal Cysteine Protease Rhodesain. Chemistry 2022; 28:e202201636. [PMID: 35852812 PMCID: PMC9826439 DOI: 10.1002/chem.202201636] [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: 05/26/2022] [Indexed: 01/11/2023]
Abstract
Rhodesain is the major cysteine protease of the protozoan parasite Trypanosoma brucei and a therapeutic target for sleeping sickness, a fatal neglected tropical disease. We designed, synthesized and characterized a bimodal activity-based probe that binds to and inactivates rhodesain. This probe exhibited an irreversible mode of action and extraordinary potency for the target protease with a kinac /Ki value of 37,000 M-1 s-1 . Two reporter tags, a fluorescent coumarin moiety and a biotin affinity label, were incorporated into the probe and enabled highly sensitive detection of rhodesain in a complex proteome by in-gel fluorescence and on-blot chemiluminescence. Furthermore, the probe was employed for microseparation and quantification of rhodesain and for inhibitor screening using a competition assay. The developed bimodal rhodesain probe represents a new proteomic tool for studying Trypanosoma pathobiochemistry and antitrypanosomal drug discovery.
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Affiliation(s)
- Carina Lemke
- Pharmaceutical InstituteDepartment of Pharmaceutical & Medicinal ChemistryUniversity of BonnAn der Immenburg 453121BonnGermany
| | - Adéla Jílková
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo n. 216610PragueCzech Republic
| | - Dominic Ferber
- Pharmaceutical InstituteDepartment of Pharmaceutical & Medicinal ChemistryUniversity of BonnAn der Immenburg 453121BonnGermany
| | - Annett Braune
- Research Group Intestinal MicrobiologyGerman Institute of Human Nutrition Potsdam-RehbrueckeArthur-Scheunert-Allee 114–11614558NuthetalGermany
| | - Anja On
- Pharmaceutical InstituteDepartment of Pharmaceutical & Medicinal ChemistryUniversity of BonnAn der Immenburg 453121BonnGermany
| | - Patrick Johe
- Institute of Pharmaceutical and Biomedical Sciences (IPBS)Johannes Gutenberg University of MainzStaudingerweg 555128MainzGermany
| | - Alena Zíková
- Biology Centre CASInstitute of ParasitologyUniversity of South BohemiaFaculty of ScienceBranišovská 1160/3137005České BudějoviceCzech Republic
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences (IPBS)Johannes Gutenberg University of MainzStaudingerweg 555128MainzGermany
| | - Michael Mareš
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo n. 216610PragueCzech Republic
| | - Martin Horn
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo n. 216610PragueCzech Republic
| | - Michael Gütschow
- Pharmaceutical InstituteDepartment of Pharmaceutical & Medicinal ChemistryUniversity of BonnAn der Immenburg 453121BonnGermany
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24
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Wang X, Zhou W, Xie W, Chen Q, Wu J. Generation of (E)-β-trifluoromethyl vinylsulfonohydrazides under photocatalysis and their anti-bacteria activity. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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From rational design to serendipity: Discovery of novel thiosemicarbazones as potent trypanocidal compounds. Eur J Med Chem 2022; 244:114876. [DOI: 10.1016/j.ejmech.2022.114876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/04/2022] [Accepted: 10/20/2022] [Indexed: 11/24/2022]
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26
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Zhu J, Li L, Drelich A, Chenna BC, Mellott DM, Taylor ZW, Tat V, Garcia CZ, Katzfuss A, Tseng CTK, Meek TD. Self-Masked Aldehyde Inhibitors of Human Cathepsin L Are Potent Anti-CoV-2 Agents. Front Chem 2022; 10:867928. [PMID: 35860632 PMCID: PMC9291521 DOI: 10.3389/fchem.2022.867928] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/12/2022] [Indexed: 12/04/2022] Open
Abstract
Cysteine proteases comprise an important class of drug targets, especially for infectious diseases such as Chagas disease (cruzain) and COVID-19 (3CL protease, cathepsin L). Peptide aldehydes have proven to be potent inhibitors for all of these proteases. However, the intrinsic, high electrophilicity of the aldehyde group is associated with safety concerns and metabolic instability, limiting the use of aldehyde inhibitors as drugs. We have developed a novel class of compounds, self-masked aldehyde inhibitors (SMAIs) which are based on the dipeptide aldehyde inhibitor (Cbz-Phe-Phe-CHO, 1), for which the P1 Phe group contains a 1′-hydroxy group, effectively, an o-tyrosinyl aldehyde (Cbz-Phe-o-Tyr-CHO, 2; (Li et al. (2021) J. Med. Chem. 64, 11,267–11,287)). Compound 2 and other SMAIs exist in aqueous mixtures as stable δ-lactols, and apparent catalysis by the cysteine protease cruzain, the major cysteine protease of Trypanosoma cruzi, results in the opening of the lactol ring to afford the aldehydes which then form reversible thiohemiacetals with the enzyme. These SMAIs are also potent, time-dependent inhibitors of human cathepsin L (Ki = 11–60 nM), an enzyme which shares 36% amino acid identity with cruzain. As inactivators of cathepsin L have recently been shown to be potent anti-SARS-CoV-2 agents in infected mammalian cells (Mellott et al. (2021) ACS Chem. Biol. 16, 642–650), we evaluated SMAIs in VeroE6 and A549/ACE2 cells infected with SARS-CoV-2. These SMAIs demonstrated potent anti-SARS-CoV-2 activity with values of EC50 = 2–8 μM. We also synthesized pro-drug forms of the SMAIs in which the hydroxyl groups of the lactols were O-acylated. Such pro-drug SMAIs resulted in significantly enhanced anti-SARS-CoV-2 activity (EC50 = 0.3–0.6 μM), demonstrating that the O-acylated-SMAIs afforded a level of stability within infected cells, and are likely converted to SMAIs by the action of cellular esterases. Lastly, we prepared and characterized an SMAI in which the sidechain adjacent to the terminal aldehyde is a 2-pyridonyl-alanine group, a mimic of both phenylalanine and glutamine. This compound (9) inhibited both cathepsin L and 3CL protease at low nanomolar concentrations, and also exerted anti-CoV-2 activity in an infected human cell line.
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Affiliation(s)
- Jiyun Zhu
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University College Station, College Station, TX, United States
| | - Linfeng Li
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University College Station, College Station, TX, United States
| | - Aleksandra Drelich
- Department of Microbiology and Immunology, John Sealy School of Medicine, University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Bala C. Chenna
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University College Station, College Station, TX, United States
| | - Drake M. Mellott
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University College Station, College Station, TX, United States
| | - Zane W. Taylor
- Department of Chemistry, College of Science, Texas A&M University College Station, College Station, TX, United States
| | - Vivian Tat
- Department of Microbiology and Immunology, John Sealy School of Medicine, University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Christopher Z. Garcia
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University College Station, College Station, TX, United States
| | - Ardala Katzfuss
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University College Station, College Station, TX, United States
| | - Chien-Te K. Tseng
- Department of Microbiology and Immunology, John Sealy School of Medicine, University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Thomas D. Meek
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University College Station, College Station, TX, United States
- *Correspondence: Thomas D. Meek,
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Previti S, Ettari R, Calcaterra E, Di Chio C, Ravichandran R, Zimmer C, Hammerschmidt S, Wagner A, Bogacz M, Cosconati S, Schirmeister T, Zappalà M. Development of Urea-Bond-Containing Michael Acceptors as Antitrypanosomal Agents Targeting Rhodesain. ACS Med Chem Lett 2022; 13:1083-1090. [PMID: 35859868 PMCID: PMC9290002 DOI: 10.1021/acsmedchemlett.2c00084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
![]()
Human African Trypanosomiasis
(HAT) is a neglected tropical disease
widespread in sub-Saharan Africa. Rhodesain, a cysteine protease of Trypanosoma brucei rhodesiense, has been identified as a
valid target for the development of anti-HAT agents. Herein, we report
a series of urea-bond-containing Michael acceptors, which were demonstrated
to be potent rhodesain inhibitors with Ki values ranging from 0.15 to 2.51 nM, and five of them showed comparable k2nd values to that of K11777, a potent antitrypanosomal
agent. Moreover, most of the urea derivatives exhibited single-digit
micromolar activity against the protozoa, and the presence of substituents
at the P3 position appears to be essential for the antitrypanosomal
effect. Replacement of Phe with Leu at the P2 site kept unchanged
the inhibitory properties. Compound 7 (SPR7) showed the
best compromise in terms of rhodesain inhibition, selectivity, and
antiparasitic activity, thus representing a new lead compound for
future SAR studies.
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Affiliation(s)
- Santo Previti
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Roberta Ettari
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Elsa Calcaterra
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Carla Di Chio
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Rahul Ravichandran
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Collin Zimmer
- Institute of Pharmaceutical and Biomedical Sciences, University of Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Stefan Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, University of Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Annika Wagner
- Institute of Organic Chemistry & Macromolecular Chemistry, Friedrich-Schiller-University of Jena, Humboldtstraße 10, 07743 Jena, Germany
| | - Marta Bogacz
- Institute of Organic Chemistry & Macromolecular Chemistry, Friedrich-Schiller-University of Jena, Humboldtstraße 10, 07743 Jena, Germany
| | - Sandro Cosconati
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, University of Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Maria Zappalà
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy
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28
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Elrufaie HA, Mohamed LM, Hamd AY, Bala NA, Elbadawi FA, Ghaboosh H, Alzain AA. Discovery of novel natural products as rhodesain inhibitors for human African trypanosomiasis using in silico techniques. J Biomol Struct Dyn 2022:1-13. [PMID: 35751127 DOI: 10.1080/07391102.2022.2092550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Human African Trypanosomiasis (HAT) or sleeping sickness is caused by the Trypanosoma brucei rhodesiense, a subspecies of the Trypanosomatide family. The parasite is associated with high morbidity and mortality rate in both animals and humans, claimed to be more fatal than other vector-transmitted diseases such as malaria. The majority of existing medications are highly toxic, not effective in the late chronic phase of the disease, and require maximum dosages to fully eradicate the parasite. In this study, we used computational methods to find out natural products that inhibit the Rhodesain, a parasitic enzyme that plays an important role in the parasite's pathogenicity, multiplication, and ability to pass through the host's blood-brain barrier. A library of 270540 natural products from ZINC databases was processed by using e-pharmacophore hypnosis and screening procedures, molecular docking, ADMET processes, and MM-GBSA calculations. This led to the identification of 3 compounds (ZINC000096269390, ZINC000035485292, and ZINC000035485242) which were then subjected to molecular dynamics. The findings of this study showed excellent binding affinity and stability toward the Rhodesain and suggest they may be a hopeful treatment for HAT in the future if further clinical trials were performed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hisham A Elrufaie
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Linda M Mohamed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Aya Y Hamd
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Noor A Bala
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | | | - Hiba Ghaboosh
- Department of Pharmaceutics, University of Gezira, Wad Madani, Sudan
| | - Abdulrahim A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
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29
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Jung S, Fuchs N, Grathwol C, Hellmich UA, Wagner A, Diehl E, Willmes T, Sotriffer C, Schirmeister T. New peptidomimetic rhodesain inhibitors with improved selectivity towards human cathepsins. Eur J Med Chem 2022; 238:114460. [PMID: 35597010 DOI: 10.1016/j.ejmech.2022.114460] [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: 04/06/2022] [Revised: 05/10/2022] [Accepted: 05/10/2022] [Indexed: 11/04/2022]
Abstract
Parasitic cysteine proteases such as rhodesain (TbCatL) from Trypanosoma brucei rhodesiense are relevant targets for developing new potential drugs against parasitic diseases (e. g. Human African Trypanosomiasis). Designing selective inhibitors for parasitic cathepsins can be challenging as they share high structural similarities with human cathepsins. In this paper, we describe the development of novel peptidomimetic rhodesain inhibitors by applying a structure-based de novo design approach and molecular docking protocols. The inhibitors with a new scaffold in P2 and P3 position display high selectivity towards trypanosomal rhodesain over human cathepsins L and B and high antitrypanosomal activity. Vinylsulfonate 2a has emerged as a potent rhodesain inhibitor (k2nd = 883 • 103 M-1 s-1) with single-digit nanomolar binding affinity (Ki = 9 nM) and more than 150-fold selectivity towards human cathepsins and it thus constitutes an interesting starting compound for the further development of selective drugs against Human African Trypanosomiasis.
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Affiliation(s)
- Sascha Jung
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudingerweg 5, Mainz, 55128, Germany
| | - Natalie Fuchs
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudingerweg 5, Mainz, 55128, Germany
| | - Christoph Grathwol
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, Karlsruhe, 76131, Germany
| | - Ute A Hellmich
- Department of Chemistry, Biochemistry Section, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 17, Mainz, 55128, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max-von-Laue-Str. 9, Frankfurt, 60438, Germany
| | - Annika Wagner
- Department of Chemistry, Biochemistry Section, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 17, Mainz, 55128, Germany
| | - Erika Diehl
- Department of Chemistry, Biochemistry Section, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 17, Mainz, 55128, Germany
| | - Thomas Willmes
- Institute of Pharmacy and Food Chemistry, University Würzburg, Am Hubland, Würzburg, 97074, Germany
| | - Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, University Würzburg, Am Hubland, Würzburg, 97074, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudingerweg 5, Mainz, 55128, Germany.
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30
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Uddin A, Gupta S, Mohammad T, Shahi D, Hussain A, Alajmi MF, El-Seedi HR, Hassan I, Singh S, Abid M. Target-Based Virtual Screening of Natural Compounds Identifies a Potent Antimalarial With Selective Falcipain-2 Inhibitory Activity. Front Pharmacol 2022; 13:850176. [PMID: 35462917 PMCID: PMC9020225 DOI: 10.3389/fphar.2022.850176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/08/2022] [Indexed: 12/02/2022] Open
Abstract
We employed a comprehensive approach of target-based virtual high-throughput screening to find potential hits from the ZINC database of natural compounds against cysteine proteases falcipain-2 and falcipain-3 (FP2 and FP3). Molecular docking studies showed the initial hits showing high binding affinity and specificity toward FP2 were selected. Furthermore, the enzyme inhibition and surface plasmon resonance assays were performed which resulted in a compound ZINC12900664 (ST72) with potent inhibitory effects on purified FP2. ST72 exhibited strong growth inhibition of chloroquine-sensitive (3D7; EC50 = 2.8 µM) and chloroquine-resistant (RKL-9; EC50 = 6.7 µM) strains of Plasmodium falciparum. Stage-specific inhibition assays revealed a delayed and growth defect during parasite growth and development in parasites treated with ST72. Furthermore, ST72 significantly reduced parasite load and increased host survival in a murine model infected with Plasmodium berghei ANKA. No Evans blue staining in ST72 treatment indicated that ST72 mediated protection of blood–brain barrier integrity in mice infected with P. berghei. ST72 did not show any significant hemolysis or cytotoxicity against human HepG2 cells suggesting a good safety profile. Importantly, ST72 with CQ resulted in improved growth inhibitory activity than individual drugs in both in vitro and in vivo studies.
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Affiliation(s)
- Amad Uddin
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Sonal Gupta
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Taj Mohammad
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Diksha Shahi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed F. Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hesham R. El-Seedi
- Department of Medicinal Chemistry, Uppsala University, Biomedical Centre, Uppsala, Sweden
| | - Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
- *Correspondence: Shailja Singh, ; Mohammad Abid,
| | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi, India
- *Correspondence: Shailja Singh, ; Mohammad Abid,
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31
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Zhang J, Wang X, Chen Q, Liu J, Zhou W, Wu J. (E)-β-Trifluoromethyl vinylsulfones as antitumor agents: Synthesis and biological evaluations. Eur J Med Chem 2022; 232:114197. [DOI: 10.1016/j.ejmech.2022.114197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/09/2022] [Indexed: 12/28/2022]
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32
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Barbosa Da Silva E, Sharma V, Hernandez-Alvarez L, Tang AH, Stoye A, O’Donoghue AJ, Gerwick WH, Payne RJ, McKerrow JH, Podust LM. Intramolecular Interactions Enhance the Potency of Gallinamide A Analogues against Trypanosoma cruzi. J Med Chem 2022; 65:4255-4269. [DOI: 10.1021/acs.jmedchem.1c02063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elany Barbosa Da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California 92093, United States
| | - Vandna Sharma
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California 92093, United States
| | - Lilian Hernandez-Alvarez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California 92093, United States
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, CEP 15054-000, Brazil
| | - Arthur H. Tang
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Alexander Stoye
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California 92093, United States
| | - William H. Gerwick
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California 92093, United States
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Richard J. Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - James H. McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California 92093, United States
| | - Larissa M. Podust
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Center for Discovery and Innovation in Parasitic Diseases, University of California San Diego, La Jolla, California 92093, United States
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33
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Bertini S, Henryon D, Edmunds AJF, Albrecht M. Pyridylidene Amide Ru Complex for Selective Oxidation in Organic Synthesis. Org Lett 2022; 24:1378-1382. [PMID: 35129978 DOI: 10.1021/acs.orglett.2c00177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ruthenium(II) bis(PYA) complex 1 (PYA = p-pyridylidene amide) is a powerful catalyst for the oxidation of sulfides to sulfones, of alkenes to carbonyl compounds, and of terminal alkynes to carboxylic acids by using NaIO4 as the terminal oxidant. The catalytic system shows a broad functional group tolerance and rate differences between alkyne and sulfide oxidation that are sufficiently large to effectively achieve selective sulfide oxidation with exquisite selectivity.
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Affiliation(s)
- Simone Bertini
- Department für Chemie, Biochemie & Pharmazie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Dorothée Henryon
- Syngenta Crop Protection Muenchwilen AG, Schaffhauseserstrasse, CH-4322 Stein, Switzerland
| | - Andrew J F Edmunds
- Syngenta Crop Protection Muenchwilen AG, Schaffhauseserstrasse, CH-4322 Stein, Switzerland
| | - Martin Albrecht
- Department für Chemie, Biochemie & Pharmazie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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34
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Huang Y, Chen D, Zheng Y, Huang S. Synthesis of 3‐Sulfonyl Indenones via Copper‐Catalyzed Redox‐Neutral Coupling Reaction. ChemistrySelect 2022. [DOI: 10.1002/slct.202104347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yuan Huang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources International Innovation Center for Forest Chemicals and Materials Nanjing Forestry University Nanjing 210037 China
| | - Dengfeng Chen
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources International Innovation Center for Forest Chemicals and Materials Nanjing Forestry University Nanjing 210037 China
| | - Yu Zheng
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources International Innovation Center for Forest Chemicals and Materials Nanjing Forestry University Nanjing 210037 China
| | - Shenlin Huang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources International Innovation Center for Forest Chemicals and Materials Nanjing Forestry University Nanjing 210037 China
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35
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Wu RZ, Zhou HY, Song JF, Xia QH, Hu W, Mou XD, Li X. Chemotherapeutics for Toxoplasma gondii: Molecular Biotargets, Binding Modes, and Structure-Activity Relationship Investigations. J Med Chem 2021; 64:17627-17655. [PMID: 34894691 DOI: 10.1021/acs.jmedchem.1c01569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Toxoplasmosis, an infectious zoonotic disease caused by the apicomplexan parasite Toxoplasma gondii (T. gondii), is a major worldwide health problem. However, there are currently no effective options (chemotherapeutic drugs or prophylactic vaccines) for treating chronic latent toxoplasmosis infection. Accordingly, seeking more effective and safer chemotherapeutics for combating this disease remains a long-term and challenging objective. In this paper, we summarize possible molecular biotargets, with an emphasis on those that are druggable and promising, including, without limitation, calcium-dependent protein kinase 1, bifunctional thymidylate synthase-dihydrofolate reductase, and farnesyl diphosphate synthase. Meanwhile, as important components of medicinal chemistry, the binding modes and structure-activity relationship profiles of the corresponding inhibitors were also illuminated. We anticipate that this information will be helpful for further identification of more effective chemotherapeutic interventions to prevent and treat zoonotic infections caused by T. gondii.
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Affiliation(s)
- Rong-Zhen Wu
- Institute of Materia Medica, Shandong First Medical University and Shandong Academy of Medical Sciences, no. 6699 Qingdao Road, Ji'nan, Shandong 250117, PR China
| | - Huai-Yu Zhou
- Department of Pathogen Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, no. 44 Wenhua Xi Road, Ji'nan, Shandong 250012, PR China
| | - Jing-Feng Song
- School of Pharmaceutical Sciences and Yunnan Provincial Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, no. 1168 Chunrong Xi Road, Kunming, Yunnan 650500, PR China
| | - Qiao-Hong Xia
- Department of Pathogen Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, no. 44 Wenhua Xi Road, Ji'nan, Shandong 250012, PR China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, no. 72 Binhai Road of JiMo, Qingdao, Shandong 266237, PR China
| | - Xiao-Dong Mou
- Institute of Materia Medica, Shandong First Medical University and Shandong Academy of Medical Sciences, no. 6699 Qingdao Road, Ji'nan, Shandong 250117, PR China
| | - Xun Li
- Institute of Materia Medica, Shandong First Medical University and Shandong Academy of Medical Sciences, no. 6699 Qingdao Road, Ji'nan, Shandong 250117, PR China.,Key Laboratory of Forensic Toxicology, Ministry of Public Security, Beijing 100192, PR China
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36
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Computer-Aided Design of Peptidomimetic Inhibitors of Falcipain-3: QSAR and Pharmacophore Models. Sci Pharm 2021. [DOI: 10.3390/scipharm89040044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In this work, antiparasitic peptidomimetics inhibitors (PEP) of falcipain-3 (FP3) of Plasmodium falciparum (Pf) are proposed using structure-based and computer-aided molecular design. Beginning with the crystal structure of PfFP3-K11017 complex (PDB ID: 3BWK), three-dimensional (3D) models of FP3-PEPx complexes with known activities ( IC50exp) were prepared by in situ modification, based on molecular mechanics and implicit solvation to compute Gibbs free energies (GFE) of inhibitor-FP3 complex formation. This resulted in a quantitative structure–activity relationships (QSAR) model based on a linear correlation between computed GFE (ΔΔGcom) and the experimentally measured IC50exp. Apart from the structure-based relationship, a ligand-based quantitative pharmacophore model (PH4) of novel PEP analogues where substitutions were directed by comparative analysis of the active site interactions was derived using the proposed bound conformations of the PEPx. This provided structural information useful for the design of virtual combinatorial libraries (VL), which was virtually screened based on the 3D-QSAR PH4. The end results were predictive inhibitory activities falling within the low nanomolar concentration range.
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37
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Santos VC, Oliveira AER, Campos ACB, Reis-Cunha JL, Bartholomeu DC, Teixeira SMR, Lima APCA, Ferreira RS. The gene repertoire of the main cysteine protease of Trypanosoma cruzi, cruzipain, reveals four sub-types with distinct active sites. Sci Rep 2021; 11:18231. [PMID: 34521898 PMCID: PMC8440672 DOI: 10.1038/s41598-021-97490-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/25/2021] [Indexed: 02/07/2023] Open
Abstract
Cruzipains are the main papain-like cysteine proteases of Trypanosoma cruzi, the protozoan parasite that causes Chagas disease. Encoded by a multigenic family, previous studies have estimated the presence of dozens of copies spread over multiple chromosomes in different parasite strains. Here, we describe the complete gene repertoire of cruzipain in three parasite strains, their genomic organization, and expression pattern throughout the parasite life cycle. Furthermore, we have analyzed primary sequence variations among distinct family members as well as structural differences between the main groups of cruzipains. Based on phylogenetic inferences and residue positions crucial for enzyme function and specificity, we propose the classification of cruzipains into two families (I and II), whose genes are distributed in two or three separate clusters in the parasite genome, according with the strain. Family I comprises nearly identical copies to the previously characterized cruzipain 1/cruzain, whereas Family II encompasses three structurally distinct sub-types, named cruzipain 2, cruzipain 3, and cruzipain 4. RNA-seq data derived from the CL Brener strain indicates that Family I genes are mainly expressed by epimastigotes, whereas trypomastigotes mainly express Family II genes. Significant differences in the active sites among the enzyme sub-types were also identified, which may play a role in their substrate selectivity and impact their inhibition by small molecules.
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Affiliation(s)
- Viviane Corrêa Santos
- grid.8430.f0000 0001 2181 4888Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brazil
| | - Antonio Edson Rocha Oliveira
- grid.8430.f0000 0001 2181 4888Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brazil ,grid.11899.380000 0004 1937 0722Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Augusto César Broilo Campos
- grid.8430.f0000 0001 2181 4888Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brazil
| | - João Luís Reis-Cunha
- grid.8430.f0000 0001 2181 4888Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brazil ,grid.8430.f0000 0001 2181 4888Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brazil
| | | | - Santuza Maria Ribeiro Teixeira
- grid.8430.f0000 0001 2181 4888Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG Brazil
| | - Ana Paula C. A. Lima
- grid.8536.80000 0001 2294 473XInstituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ Brazil
| | - Rafaela Salgado Ferreira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
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38
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Friday SN, Cheng DW, Zagler SG, Zanella BS, Dietz JD, Calbat CN, Roach LT, Bagnal C, Faile IS, Halkides CJ, Viola RE. Design and testing of selective inactivators against an antifungal enzyme target. Drug Dev Res 2021; 83:447-460. [PMID: 34469014 DOI: 10.1002/ddr.21875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/03/2021] [Accepted: 08/19/2021] [Indexed: 11/10/2022]
Abstract
Systemic infections from fungal organisms are becoming increasingly difficult to treat as drug resistance continues to emerge. To substantially expand the antifungal drug landscape new compounds must be identified and developed with novel modes of action against previously untested drug targets. Most drugs block the activity of their targets through reversible, noncovalent interactions. However, a significant number of drugs form irreversible, covalent bonds with their selected targets. While more challenging to develop, these irreversible inactivators offer some significant advantages as novel antifungal agents. Vinyl sulfones contain a potentially reactive functional group that could function as a selective enzyme inactivator, and members of this class of compounds are now being developed as inactivators against an antifungal drug target. The enzyme aspartate semialdehyde dehydrogenase (ASADH) catalyzes a key step in an essential microbial pathway and is essential for the survival of every microorganism examined. A series of vinyl sulfones have been designed, guided by molecular modeling and docking studies to enhance their affinity for fungal ASADHs. These newly synthesized compounds have been examined against this target enzyme from the pathogenic fungal organism Candida albicans. Vinyl sulfones containing complementary structural elements inhibit this enzyme with inhibition constants in the low-micromolar range. These inhibitors have also led to the rapid and irreversible inactivation of this enzyme, and show some initial selectivity when compared to the inactivation of a bacterial ASADH. The best inactivators will serve as lead compounds for the development of potent and selective antifungal agents.
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Affiliation(s)
- Samantha N Friday
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio, USA
| | - Daniel W Cheng
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Sebastian G Zagler
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Brady S Zanella
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Jordan D Dietz
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Christopher N Calbat
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Logan T Roach
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Cindy Bagnal
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Ian S Faile
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Christopher J Halkides
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina, USA
| | - Ronald E Viola
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio, USA
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39
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Li L, Chenna BC, Yang KS, Cole TR, Goodall ZT, Giardini M, Moghadamchargari Z, Hernandez EA, Gomez J, Calvet CM, Bernatchez JA, Mellott DM, Zhu J, Rademacher A, Thomas D, Blankenship LR, Drelich A, Laganowsky A, Tseng CTK, Liu WR, Wand AJ, Cruz-Reyes J, Siqueira-Neto JL, Meek TD. Self-Masked Aldehyde Inhibitors: A Novel Strategy for Inhibiting Cysteine Proteases. J Med Chem 2021; 64:11267-11287. [PMID: 34288674 PMCID: PMC10504874 DOI: 10.1021/acs.jmedchem.1c00628] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cysteine proteases comprise an important class of drug targets, especially for infectious diseases such as Chagas disease (cruzain) and COVID-19 (3CL protease, cathepsin L). Peptide aldehydes have proven to be potent inhibitors for all of these proteases. However, the intrinsic, high electrophilicity of the aldehyde group is associated with safety concerns and metabolic instability, limiting the use of aldehyde inhibitors as drugs. We have developed a novel class of self-masked aldehyde inhibitors (SMAIs) for cruzain, the major cysteine protease of the causative agent of Chagas disease-Trypanosoma cruzi. These SMAIs exerted potent, reversible inhibition of cruzain (Ki* = 18-350 nM) while apparently protecting the free aldehyde in cell-based assays. We synthesized prodrugs of the SMAIs that could potentially improve their pharmacokinetic properties. We also elucidated the kinetic and chemical mechanism of SMAIs and applied this strategy to the design of anti-SARS-CoV-2 inhibitors.
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Affiliation(s)
- Linfeng Li
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Bala C Chenna
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Kai S Yang
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
| | - Taylor R Cole
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Zachary T Goodall
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Miriam Giardini
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093, United States
| | - Zahra Moghadamchargari
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
| | - Elizabeth A Hernandez
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Jana Gomez
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Claudia M Calvet
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093, United States
| | - Jean A Bernatchez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093, United States
| | - Drake M Mellott
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Jiyun Zhu
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Andrew Rademacher
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Diane Thomas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093, United States
| | - Lauren R Blankenship
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
| | - Aleksandra Drelich
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas 77555, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
| | - Chien-Te K Tseng
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas 77555, United States
| | - Wenshe R Liu
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
| | - A Joshua Wand
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Jair L Siqueira-Neto
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093, United States
| | - Thomas D Meek
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
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40
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Jung S, Fuchs N, Johe P, Wagner A, Diehl E, Yuliani T, Zimmer C, Barthels F, Zimmermann RA, Klein P, Waigel W, Meyr J, Opatz T, Tenzer S, Distler U, Räder HJ, Kersten C, Engels B, Hellmich UA, Klein J, Schirmeister T. Fluorovinylsulfones and -Sulfonates as Potent Covalent Reversible Inhibitors of the Trypanosomal Cysteine Protease Rhodesain: Structure-Activity Relationship, Inhibition Mechanism, Metabolism, and In Vivo Studies. J Med Chem 2021; 64:12322-12358. [PMID: 34378914 DOI: 10.1021/acs.jmedchem.1c01002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Rhodesain is a major cysteine protease of Trypanosoma brucei rhodesiense, a pathogen causing Human African Trypanosomiasis, and a validated drug target. Recently, we reported the development of α-halovinylsulfones as a new class of covalent reversible cysteine protease inhibitors. Here, α-fluorovinylsulfones/-sulfonates were optimized for rhodesain based on molecular modeling approaches. 2d, the most potent and selective inhibitor in the series, shows a single-digit nanomolar affinity and high selectivity toward mammalian cathepsins B and L. Enzymatic dilution assays and MS experiments indicate that 2d is a slow-tight binder (Ki = 3 nM). Furthermore, the nonfluorinated 2d-(H) shows favorable metabolism and biodistribution by accumulation in mice brain tissue after intraperitoneal and oral administration. The highest antitrypanosomal activity was observed for inhibitors with an N-terminal 2,3-dihydrobenzo[b][1,4]dioxine group and a 4-Me-Phe residue in P2 (2e/4e) with nanomolar EC50 values (0.14/0.80 μM). The different mechanisms of reversible and irreversible inhibitors were explained using QM/MM calculations and MD simulations.
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Affiliation(s)
- Sascha Jung
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Natalie Fuchs
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Patrick Johe
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Annika Wagner
- Department of Chemistry, Biochemistry Section, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
| | - Erika Diehl
- Department of Chemistry, Biochemistry Section, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
| | - Tri Yuliani
- Institute for Pharmacology and Clinical Pharmacy, Goethe University, Max-von-Laue-Str. 9, 60439 Frankfurt, Germany
| | - Collin Zimmer
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Fabian Barthels
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Philipp Klein
- Department of Chemistry, Organic Chemistry Section, Johannes Gutenberg University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Waldemar Waigel
- Department of Physical and Theoretical Chemistry, Julius-Maximilians-University, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Jessica Meyr
- Department of Physical and Theoretical Chemistry, Julius-Maximilians-University, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Till Opatz
- Department of Chemistry, Organic Chemistry Section, Johannes Gutenberg University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Stefan Tenzer
- Institute for Immunology, University Medical Center, Johannes Gutenberg University, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Ute Distler
- Institute for Immunology, University Medical Center, Johannes Gutenberg University, Langenbeckstraße 1, 55131 Mainz, Germany
| | - Hans-Joachim Räder
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Bernd Engels
- Department of Physical and Theoretical Chemistry, Julius-Maximilians-University, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Ute A Hellmich
- Department of Chemistry, Biochemistry Section, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany.,Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Jochen Klein
- Institute for Pharmacology and Clinical Pharmacy, Goethe University, Max-von-Laue-Str. 9, 60439 Frankfurt, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
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41
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Arafet K, González FV, Moliner V. Elucidating the Dual Mode of Action of Dipeptidyl Enoates in the Inhibition of Rhodesain Cysteine Proteases. Chemistry 2021; 27:10142-10150. [PMID: 33852187 DOI: 10.1002/chem.202100892] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 01/06/2023]
Abstract
A computational study of the two possible inhibition mechanisms of rhodesain cysteine protease by the dipeptidyl enoate Cbz-Phe-Leu-CH=CH-CO2 C2 H5 has been carried out by means of molecular dynamics simulations with hybrid QM/MM potentials. The low free energy barriers confirm that the Cys25 residue can attack both Cβ and C1 atoms of the inhibitor, confirming a dual mode of action in the inhibition of the rhodesain by enoates. According to the results, the inhibition process through the Cys25 attack on the Cβ atom of the inhibitor is an exergonic and irreversible process, while the inhibition process when Cys25 attacks on the C1 atom of the inhibitor is and exergonic but reversible process. The interactions between the inhibitor and rhodesain suggest that P2 is the most important fragment to consider in the design of new efficient inhibitors of rhodesain. These results may be useful for the design of new inhibitors of rhodesain and other related cysteine proteases based on dipeptidyl enoates scaffolds.
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Affiliation(s)
- Kemel Arafet
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castelló, Spain
| | - Florenci V González
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12071, Castelló, Spain
| | - Vicent Moliner
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071, Castelló, Spain
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42
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Ettari R, Previti S, Di Chio C, Zappalà M. Falcipain-2 and Falcipain-3 Inhibitors as Promising Antimalarial Agents. Curr Med Chem 2021; 28:3010-3031. [PMID: 32744954 DOI: 10.2174/0929867327666200730215316] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/01/2020] [Accepted: 07/11/2020] [Indexed: 11/22/2022]
Abstract
Malaria remains a serious problem in global public health, particularly widespread in South America and in tropical regions of Africa and Asia. Chemotherapy is actually the only way to treat this poverty-related disease, since an effective vaccine is not currently available. However, the onset of resistance to the most common antimalarial drugs sometimes makes the current therapeutic regimen problematic. Therefore, the identification of new targets for a new drug discovery process is an urgent priority. In this context, falcipain-2 and falcipain- 3 of P. falciparum represent the key enzymes in the life-cycle of the parasite. Both falcipain- 2 and falcipain-3 are involved in hemoglobin hydrolysis, an essential pathway to provide free amino acids for the parasite metabolic needs. In addition, falcipain-2 is involved in cleaving ankirin and band 4.1 protein, which are cytoskeletal elements essential for the stability of the red cell membrane. This review article is focused on the most recent and effective inhibitors of falcipain-2 and falcipain-3, with particular attention to peptide, peptidomimetic or nonpeptide inhibitors, which targeted one or both the malarial cysteine proteases, endowed with a consistent activity against P. falciparum.
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Affiliation(s)
- Roberta Ettari
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Annunziata, 98168 Messina, Italy
| | - Santo Previti
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Annunziata, 98168 Messina, Italy
| | - Carla Di Chio
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Annunziata, 98168 Messina, Italy
| | - Maria Zappalà
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Annunziata, 98168 Messina, Italy
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43
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Craven GB, Briggs EL, Zammit CM, McDermott A, Greed S, Affron DP, Leinfellner C, Cudmore HR, Tweedy RR, Luisi R, Bull JA, Armstrong A. Synthesis and Configurational Assignment of Vinyl Sulfoximines and Sulfonimidamides. J Org Chem 2021; 86:7403-7424. [PMID: 34003635 DOI: 10.1021/acs.joc.1c00373] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Vinyl sulfones and sulfonamides are valued for their use as electrophilic warheads in covalent protein inhibitors. Conversely, the S(VI) aza-isosteres thereof, vinyl sulfoximines and sulfonimidamides, are far less studied and have yet to be applied to the field of protein bioconjugation. Herein, we report a range of different synthetic methodologies for constructing vinyl sulfoximine and vinyl sulfonimidamide architectures that allows access to new areas of electrophilic chemical space. We demonstrate how late-stage functionalization can be applied to these motifs to incorporate alkyne tags, generating fully functionalized probes for future chemical biology applications. Finally, we establish a workflow for determining the absolute configuration of enantioenriched vinyl sulfoximines and sulfonimidamides by comparing experimentally and computationally determined electronic circular dichroism spectra, enabling access to configurationally assigned enantiomeric pairs by separation.
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Affiliation(s)
- Gregory B Craven
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K.,The Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Edward L Briggs
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Charlotte M Zammit
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Alexander McDermott
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Stephanie Greed
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Dominic P Affron
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Charlotte Leinfellner
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Hannah R Cudmore
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Ruth R Tweedy
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Renzo Luisi
- Department of Pharmacy-Drug Sciences, University of Bari, "A. Moro" Via E. Orabona 4, Bari 70125, Italy
| | - James A Bull
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Alan Armstrong
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
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44
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Jílková A, Rubešová P, Fanfrlík J, Fajtová P, Řezáčová P, Brynda J, Lepšík M, Mertlíková-Kaiserová H, Emal CD, Renslo AR, Roush WR, Horn M, Caffrey CR, Mareš M. Druggable Hot Spots in the Schistosomiasis Cathepsin B1 Target Identified by Functional and Binding Mode Analysis of Potent Vinyl Sulfone Inhibitors. ACS Infect Dis 2021; 7:1077-1088. [PMID: 33175511 PMCID: PMC8154419 DOI: 10.1021/acsinfecdis.0c00501] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Schistosomiasis, a parasitic disease
caused by blood flukes of
the genus Schistosoma, is a global health problem
with over 200 million people infected. Treatment relies on just one
drug, and new chemotherapies are needed. Schistosoma mansoni cathepsin B1 (SmCB1) is a critical peptidase for the digestion of
host blood proteins and a validated drug target. We screened a library
of peptidomimetic vinyl sulfones against SmCB1 and identified the
most potent SmCB1 inhibitors reported to date that are active in the
subnanomolar range with second order rate constants (k2nd) of ∼2 × 105 M–1 s–1. High resolution crystal structures of the
two best inhibitors in complex with SmCB1 were determined. Quantum
chemical calculations of their respective binding modes identified
critical hot spot interactions in the S1′ and S2 subsites.
The most potent inhibitor targets the S1′ subsite with an N-hydroxysulfonic amide moiety and displays favorable functional
properties, including bioactivity against the pathogen, selectivity
for SmCB1 over human cathepsin B, and reasonable metabolic stability.
Our results provide structural insights for the rational design of
next-generation SmCB1 inhibitors as potential drugs to treat schistosomiasis.
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Affiliation(s)
- Adéla Jílková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Petra Rubešová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Pavla Fajtová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Helena Mertlíková-Kaiserová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Cory D. Emal
- Eastern Michigan University, 541 Mark Jefferson, Ypsilanti, Michigan 48197, United States
| | - Adam R. Renslo
- University of California San Francisco, 600 16th Street, San Francisco, California 94143, United States
| | - William R. Roush
- The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
| | - Conor R. Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael Mareš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 16610 Prague, Czech Republic
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45
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Seok JK, Kang HC, Cho YY, Lee HS, Lee JY. Therapeutic regulation of the NLRP3 inflammasome in chronic inflammatory diseases. Arch Pharm Res 2021; 44:16-35. [PMID: 33534121 PMCID: PMC7884371 DOI: 10.1007/s12272-021-01307-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/07/2021] [Indexed: 12/13/2022]
Abstract
Inflammasomes are cytosolic pattern recognition receptors that recognize pathogen-associated molecular patterns (PAMPs) and danger-associated molecular patterns (DAMPs) derived from invading pathogens and damaged tissues, respectively. Upon activation, the inflammasome forms a complex containing a receptor protein, an adaptor, and an effector to induce the autocleavage and activation of procaspase-1 ultimately culminating in the maturation and secretion of IL-1β and IL-18 and pyroptosis. Inflammasome activation plays an important role in host immune responses to pathogen infections and tissue repair in response to cellular damage. The NLRP3 inflammasome is a well-characterized pattern recognition receptor and is well known for its critical role in the regulation of immunity and the development and progression of various inflammatory diseases. In this review, we summarize recent efforts to develop therapeutic applications targeting the NLRP3 inflammasome to cure and prevent chronic inflammatory diseases. This review extensively discusses NLRP3 inflammasome-related diseases and current development of small molecule inhibitors providing beneficial information on the design of therapeutic strategies for NLRP3 inflammasome-related diseases. Additionally, small molecule inhibitors are classified depending on direct or indirect targeting mechanism to describe the current status of the development of pharmacological inhibitors.
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Affiliation(s)
- Jin Kyung Seok
- BK21 PLUS Team, College of Pharmacy, The Catholic University of Korea, Bucheon, 14662, Republic of Korea
| | - Han Chang Kang
- BK21 PLUS Team, College of Pharmacy, The Catholic University of Korea, Bucheon, 14662, Republic of Korea
| | - Yong-Yeon Cho
- BK21 PLUS Team, College of Pharmacy, The Catholic University of Korea, Bucheon, 14662, Republic of Korea
| | - Hye Suk Lee
- BK21 PLUS Team, College of Pharmacy, The Catholic University of Korea, Bucheon, 14662, Republic of Korea
| | - Joo Young Lee
- BK21 PLUS Team, College of Pharmacy, The Catholic University of Korea, Bucheon, 14662, Republic of Korea.
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46
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Tu X, Huang J, Xie W, Zhu T, Wu J. Generation of (E)-β-sulfonyl enamines from sulfur dioxide via a radical process. Org Chem Front 2021. [DOI: 10.1039/d0qo01551b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
An iron(ii)-catalyzed three-component reaction of O-acyl oximes, sulfur dioxide, and N-vinylacetamides is accomplished. Diverse (E)-β-sulfonyl enamines are obtained in moderate to good yields by using this protocol with excellent stereoselectivity and regioselectivity.
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Affiliation(s)
- Xiaodong Tu
- School of Chemistry and Chemical Engineering
- Hunan University of Science and Technology
- Xiangtan 411201
- China
| | - Jiapian Huang
- School of Pharmaceutical and Materials Engineering & Institute for Advanced Studies
- Taizhou University
- Taizhou 318000
- China
| | - Wenlin Xie
- School of Chemistry and Chemical Engineering
- Hunan University of Science and Technology
- Xiangtan 411201
- China
| | - Tonghao Zhu
- School of Pharmaceutical and Materials Engineering & Institute for Advanced Studies
- Taizhou University
- Taizhou 318000
- China
| | - Jie Wu
- School of Pharmaceutical and Materials Engineering & Institute for Advanced Studies
- Taizhou University
- Taizhou 318000
- China
- State Key Laboratory of Organometallic Chemistry
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47
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Johé P, Jaenicke E, Neuweiler H, Schirmeister T, Kersten C, Hellmich UA. Structure, interdomain dynamics, and pH-dependent autoactivation of pro-rhodesain, the main lysosomal cysteine protease from African trypanosomes. J Biol Chem 2021; 296:100565. [PMID: 33745969 PMCID: PMC8080524 DOI: 10.1016/j.jbc.2021.100565] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/18/2021] [Accepted: 03/17/2021] [Indexed: 02/06/2023] Open
Abstract
Rhodesain is the lysosomal cathepsin L-like cysteine protease of Trypanosoma brucei rhodesiense, the causative agent of Human African Trypanosomiasis. The enzyme is essential for the proliferation and pathogenicity of the parasite as well as its ability to overcome the blood-brain barrier of the host. Lysosomal cathepsins are expressed as zymogens with an inactivating prodomain that is cleaved under acidic conditions. A structure of the uncleaved maturation intermediate from a trypanosomal cathepsin L-like protease is currently not available. We thus established the heterologous expression of T. brucei rhodesiense pro-rhodesain in Escherichia coli and determined its crystal structure. The trypanosomal prodomain differs from nonparasitic pro-cathepsins by a unique, extended α-helix that blocks the active site and whose side-chain interactions resemble those of the antiprotozoal inhibitor K11777. Interdomain dynamics between pro- and core protease domain as observed by photoinduced electron transfer fluorescence correlation spectroscopy increase at low pH, where pro-rhodesain also undergoes autocleavage. Using the crystal structure, molecular dynamics simulations, and mutagenesis, we identify a conserved interdomain salt bridge that prevents premature intramolecular cleavage at higher pH values and may thus present a control switch for the observed pH sensitivity of proenzyme cleavage in (trypanosomal) CathL-like proteases.
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Affiliation(s)
- Patrick Johé
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
| | - Elmar Jaenicke
- Institute for Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
| | - Hannes Neuweiler
- Department for Biotechnology and Biophysics, Julius-Maximilians-University, Würzburg, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany.
| | - Ute A Hellmich
- Department of Chemistry, Biochemistry Division, Johannes Gutenberg-University, Mainz, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt, Germany.
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48
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Ibrahim M, Latif A, Ammara, Ali A, Ribeiro AI, Farooq U, Ullah F, Khan A, Al-Harrasi A, Ahmad M, Ali M. Macrocyclic sulfone derivatives: Synthesis, characterization, in vitro biological evaluation and molecular docking. Drug Dev Res 2020; 82:562-574. [PMID: 33368483 DOI: 10.1002/ddr.21775] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/28/2020] [Accepted: 12/02/2020] [Indexed: 11/10/2022]
Abstract
An artificial series of macrocycles based on 4,4'-sulfonyldiphenol intermediate was synthesized using a multistep procedure involving oxidation of bisphenol sulfide, etherification of phenolic hydroxyl groups, and final ring closure with different diamines. Different chemical species having aromatic, heteroaromatic, and aliphatic characters were incorporated into macrocyclic frameworks in the final step of ring closure. This simple and easily executable synthetic strategy was applied to synthesize 15 macrocycles (5a-o) in excellent yields. Characterization of the synthesized products was achieved through well-known modern spectroscopic techniques such as IR, NMR, and Mass. Macrocycles 5m and 5n were found to show significant AChE inhibition with IC50 values of 76.9 ± 0.24 and 71.2 ± 0.77 μM, respectively. Macrocycle 5n was also found to be an active inhibitor of butyrylcholinesterase (BChE) with IC50 score of 55.3 ± 0.54 μM. Among others, macrocycle 5l cyclized with o-phenylenediamine demonstrated moderate inhibition with IC50 value of 81.1 ± 0.54 μM. Increasing interest in studying interactions of macrocycles with different enzymatic targets compelled us to design and synthesize sulfone-based macrocycles that might prove as highly potent class of biologically active compounds.
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Affiliation(s)
- Muhammad Ibrahim
- Department of Chemistry, University of Malakand, Chakdara 18800, Dir Lower, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Latif
- Department of Chemistry, University of Malakand, Chakdara 18800, Dir Lower, Khyber Pakhtunkhwa, Pakistan
| | - Ammara
- Department of Chemistry, University of Malakand, Chakdara 18800, Dir Lower, Khyber Pakhtunkhwa, Pakistan
| | - Akbar Ali
- Department of Chemistry, University of Sargodha, Sargodha, 40100, Pakistan
| | - Alany Ingrid Ribeiro
- Department of Chemistry, Federal University of São Carlos, Rod. Washington Luís, Km 265, São Carlos, Brazil
| | - Umar Farooq
- Department of Chemistry, COMSATS University Islamabad, Islamabad Campus, Pakistan
| | - Farhat Ullah
- Department of Pharmacy, University of Malakand, Chakdara, Pakistan
| | - Ajmal Khan
- Natural and Medical Sciences Research Centre, University of Nizwa, PO Box 33, 616 Birkat Al Mauz, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, PO Box 33, 616 Birkat Al Mauz, Nizwa, Oman
| | - Manzoor Ahmad
- Department of Chemistry, University of Malakand, Chakdara 18800, Dir Lower, Khyber Pakhtunkhwa, Pakistan
| | - Mumtaz Ali
- Department of Chemistry, University of Malakand, Chakdara 18800, Dir Lower, Khyber Pakhtunkhwa, Pakistan
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49
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Mishra M, Singh V, Tellis MB, Joshi RS, Pandey KC, Singh S. Cyclic peptide engineered from phytocystatin inhibitory hairpin loop as an effective modulator of falcipains and potent antimalarial. J Biomol Struct Dyn 2020; 40:3642-3654. [PMID: 33292080 DOI: 10.1080/07391102.2020.1848629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Cystatins are classical competitive inhibitors of C1 family cysteine proteases (papain family). Phytocystatin superfamily shares high sequence homology and typical tertiary structure with conserved glutamine-valine-glycine (Q-X-V-X-G) loop blocking the active site of C1 proteases. Here, we develop a cysteine-bounded cyclic peptide (CYS-cIHL) and linear peptide (CYS-IHL), using the conserved inhibitory hairpin loop amino acid sequence. Using an in silico approach based on modeling, protein-peptide docking, molecular dynamics simulations and calculation of free energy of binding, we designed and validated inhibitory peptides against falcipain-2 (FP-2) and -3 (FP-3), cysteine proteases from the malarial parasite Plasmodium falciparum. Falcipains are critical hemoglobinases of P. falciparum that are validated targets for the development of antimalarial therapies. CYS-cIHL was able to bind with micromolar affinity to FP-2 and modulate its binding with its substrate, hemoglobin in in vitro and in vivo assays. CYS-cIHL could effectively block parasite growth and displayed antimalarial activity in culture assays with no cytotoxicity towards human cells. These results indicated that cyclization can substantially increase the peptide affinity to the target. Furthermore, this can be applied as an effective strategy for engineering peptide inhibitory potency against proteases.
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Affiliation(s)
- Manasi Mishra
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Uttar Pradesh, India
| | - Vigyasa Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Meenakshi B Tellis
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Rakesh S Joshi
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kailash C Pandey
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, Dwarka, India
| | - Shailja Singh
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Uttar Pradesh, India.,Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
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50
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Doherty W, Adler N, Butler TJ, Knox AJS, Evans P. Synthesis and optimisation of P 3 substituted vinyl sulfone-based inhibitors as anti-trypanosomal agents. Bioorg Med Chem 2020; 28:115774. [PMID: 32992251 DOI: 10.1016/j.bmc.2020.115774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 10/23/2022]
Abstract
A series of lysine-based vinyl sulfone peptidomimetics were synthesised and evaluated for anti-trypanosomal activity against bloodstream forms of T. brucei. This focused set of compounds, varying in the P3 position, were accessed in a divergent manner from a common intermediate (ammonium salt 8). Several P3 analogues exhibited sub-micromolar EC50 values, with thiourea 14, urea 15 and amide 21 representing the most potent anti-trypanosomal derivatives of the series. In order to establish an in vitro selectivity index the most active anti-trypanosomal compounds were also assessed for their impact on cell viability and cytotoxity effects in mammalian cells. Encouragingly, all compounds only reduced cellular metabolic activity in mammalian cells to a modest level and little, or no cytotoxicity, was observed with the series.
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Affiliation(s)
- William Doherty
- Centre for Synthesis and Chemical Biology, School of Chemistry and Chemical Biology, University College Dublin, Dublin D04 N2E2, Ireland
| | - Nikoletta Adler
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Pearse Street, Dublin 2, Ireland
| | - Thomas J Butler
- School of Biological and Health Sciences, Technological University Dublin, Dublin City Campus, Kevin St., Dublin D08 NF82, Ireland
| | - Andrew J S Knox
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Pearse Street, Dublin 2, Ireland; School of Biological and Health Sciences, Technological University Dublin, Dublin City Campus, Kevin St., Dublin D08 NF82, Ireland.
| | - Paul Evans
- Centre for Synthesis and Chemical Biology, School of Chemistry and Chemical Biology, University College Dublin, Dublin D04 N2E2, Ireland.
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