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Article ; Online: Differential specificity of SARS-CoV-2 main protease variants on peptide versus protein-based substrates.

Rocho, Fernanda R / Snipas, Scott J / Shamim, Anwar / Rut, Wioletta / Drag, Marcin / Montanari, Carlos A / Salvesen, Guy S

The FEBS journal

2023 Volume 291, Issue 1, Page(s) 61–69

Abstract: The SARS-CoV-2 main protease ( ... ...

Abstract	The SARS-CoV-2 main protease (M
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/genetics ; Viral Nonstructural Proteins/genetics ; Peptides/genetics ; Coronavirus 3C Proteases/genetics ; Protease Inhibitors/chemistry ; Antiviral Agents/pharmacology ; Peptide Hydrolases
Chemical Substances	3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Viral Nonstructural Proteins ; Peptides ; Coronavirus 3C Proteases (EC 3.4.22.28) ; Protease Inhibitors ; Antiviral Agents ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2023-11-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16970
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Article ; Online: Antioxidant and anti-sickling activity of glucal-based triazoles compounds - An in vitro and in silico study.

Vieira Veloso, Rodinei / Shamim, Anwar / Lamarrey, Yann / Stefani, Hélio A / Mozer Sciani, Juliana

Bioorganic chemistry

2021 Volume 109, Page(s) 104709

Abstract: The sickle cell disease (SCD) has a genetic cause, characterized by a replacement of glutamic acid to valine in the β-chain of hemoglobin. The disease has no effective treatment so far, and patients suffer a range from acute to chronic complications that ...

Abstract	The sickle cell disease (SCD) has a genetic cause, characterized by a replacement of glutamic acid to valine in the β-chain of hemoglobin. The disease has no effective treatment so far, and patients suffer a range from acute to chronic complications that include chronic hemolytic anemia, vaso-occlusive ischemia, pain, acute thoracic syndrome, cerebrovascular accident, nephropathy, osteonecrosis and reduced lifetime. The oxidation in certain regions of the hemoglobin favors the reactive oxygen species (ROS) formation, which is the cause of many clinical manifestations. Antioxidants have been studied to reduce the hemoglobin ROS levels, and in this sense, we have searched for new antioxidants glucal-based triazoles compounds with anti-sickling activity. Thirty analogues were synthetized and tested in in vitro antioxidant assays. Two of them were selected based in their effects and concentration-response activity and conducted to in cell assays. Both molecules did not cause any hemolysis and could reduce the red blood cell damage caused by hydrogen peroxide, in a model of oxidative stress induction that mimics the SCD. Moreover, one molecule (termed 11m), besides reducing the hemolysis, was able to prevent the cell damage caused by the hydrogen peroxide. Later on, by in silico pharmacokinetics analysis, we could see that 11m has appropriated proprieties for druggability and the probable mechanism of action is the binding to Peroxiredoxin-5, an antioxidant enzyme that reduces the hydrogen peroxide levels, verified after molecular docking assays. Thus, starting from 30 glucal-based triazoles molecules in a structure-activity relationship, we could select one with antioxidant proprieties that could act on RBC to reduce the oxidative stress, being useful for the treatment of SCD.
MeSH term(s)	Anemia, Sickle Cell/drug therapy ; Antioxidants/chemistry ; Antioxidants/pharmacology ; Calcium Gluconate/chemistry ; Drug Discovery ; Erythrocytes/drug effects ; Humans ; Models, Molecular ; Molecular Docking Simulation ; Molecular Structure ; Oxidative Stress/drug effects ; Structure-Activity Relationship ; Triazoles/chemistry ; Triazoles/pharmacology
Chemical Substances	Antioxidants ; Triazoles ; Calcium Gluconate (SQE6VB453K)
Language	English
Publishing date	2021-02-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120080-x
ISSN	1090-2120 ; 0045-2068
ISSN (online)	1090-2120
ISSN	0045-2068
DOI	10.1016/j.bioorg.2021.104709
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Article ; Online: Predicting the Relative Binding Affinity for Reversible Covalent Inhibitors by Free Energy Perturbation Calculations.

Bonatto, Vinícius / Shamim, Anwar / Rocho, Fernanda Dos R / Leitão, Andrei / Luque, F Javier / Lameira, Jerônimo / Montanari, Carlos A

Journal of chemical information and modeling

2021 Volume 61, Issue 9, Page(s) 4733–4744

Abstract: Covalent inhibitors are assuming central importance in drug discovery projects, especially in this pandemic scenario. Many research groups have focused their attention on inhibiting viral proteases or human proteases such as cathepsin L (hCatL). The ... ...

Abstract	Covalent inhibitors are assuming central importance in drug discovery projects, especially in this pandemic scenario. Many research groups have focused their attention on inhibiting viral proteases or human proteases such as cathepsin L (hCatL). The inhibition of these critical enzymes may impair viral replication. However, molecular modeling of covalent ligands is challenging since covalent and noncovalent ligand-bound states must be considered in the binding process. In this work, we evaluated the suitability of free energy perturbation (FEP) calculations as a tool for predicting the binding affinity of reversible covalent inhibitors of hCatL. Our strategy relies on the relative free energy calculated for both covalent and noncovalent complexes and the free energy changes have been compared with experimental data for eight nitrile-based inhibitors, including three new inhibitors of hCatL. Our results demonstrate that the covalent complex can be employed to properly rank the inhibitors. Nevertheless, a comparison of the free energy changes in both noncovalent and covalent states is valuable to interpret the effect triggered by the formation of the covalent bond on the interactions played by functional groups distant from the warhead. Overall, FEP can be employed as a powerful predictor tool in developing and understanding the activity of reversible covalent inhibitors.
MeSH term(s)	Drug Discovery ; Entropy ; Humans ; Ligands ; Models, Molecular ; Thermodynamics
Chemical Substances	Ligands
Language	English
Publishing date	2021-08-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.1c00515
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Article ; Online: Design, synthesis and stepwise optimization of nitrile-based inhibitors of cathepsins B and L.

Cianni, Lorenzo / Rocho, Fernanda Dos Reis / Bonatto, Vinícius / Martins, Felipe Cardoso Prado / Lameira, Jerônimo / Leitão, Andrei / Montanari, Carlos A / Shamim, Anwar

Bioorganic & medicinal chemistry

2020 Volume 29, Page(s) 115827

Abstract: Human cathepsin B (CatB) is an important biological target in cancer therapy. In this work, we performed a knowledge-based design approach and the synthesis of a new set of 19 peptide-like nitrile-based cathepsin inhibitors. Reported compounds were ... ...

Abstract	Human cathepsin B (CatB) is an important biological target in cancer therapy. In this work, we performed a knowledge-based design approach and the synthesis of a new set of 19 peptide-like nitrile-based cathepsin inhibitors. Reported compounds were assayed against a panel of human cysteine proteases: CatB, CatL, CatK, and CatS. Three compounds (7h, 7i, and 7j) displayed nanomolar inhibition of CatB and selectivity over CatK and CatL. The selectivity was achieved by using the combination of a para biphenyl ring at P3, halogenated phenylalanine in P2 and Thr-O-Bz group at P1. Likewise, compounds 7i and 7j showed selective CatB inhibition among the panel of enzymes studied. We have also described a successful example of bioisosteric replacement of the amide bond for a sulfonamide one [7e → 6b], where we observed an increase in affinity and selectivity for CatB while lowering the compound lipophilicity (ilogP). Our knowledge-based design approach and the respective structure-activity relationships provide insights into the specific ligand-target interactions for therapeutically relevant cathepsins.
MeSH term(s)	Amides/chemical synthesis ; Amides/chemistry ; Amides/pharmacology ; Amines/chemical synthesis ; Amines/chemistry ; Amines/pharmacology ; Cathepsin B/antagonists & inhibitors ; Cathepsin B/metabolism ; Cathepsin L/antagonists & inhibitors ; Cathepsin L/metabolism ; Dose-Response Relationship, Drug ; Drug Design ; Enzyme Inhibitors/chemical synthesis ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Humans ; Molecular Dynamics Simulation ; Molecular Structure ; Structure-Activity Relationship
Chemical Substances	Amides ; Amines ; Enzyme Inhibitors ; CTSB protein, human (EC 3.4.22.1) ; Cathepsin B (EC 3.4.22.1) ; CTSL protein, human (EC 3.4.22.15) ; Cathepsin L (EC 3.4.22.15)
Language	English
Publishing date	2020-11-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1161284-8
ISSN	1464-3391 ; 0968-0896
ISSN (online)	1464-3391
ISSN	0968-0896
DOI	10.1016/j.bmc.2020.115827
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Article ; Online: Dipeptidyl nitrile derivatives suppress the Trypanosoma cruzi in vitro infection.

Quilles, José C / Shamim, Anwar / Tezuka, Daiane Y / Batista, Pedro H J / Lopes, Carla D / de Albuquerque, Sérgio / Montanari, Carlos A / Leitão, Andrei

Experimental parasitology

2020 Volume 219, Page(s) 108032

Abstract: Chagas disease affects several countries around the world with health and sanitation problems. Cysteine proteases are essential for the virulence and replication of the Trypanosoma cruzi, being modulated by dipeptidyl nitriles and derivatives. Here, four ...

Abstract	Chagas disease affects several countries around the world with health and sanitation problems. Cysteine proteases are essential for the virulence and replication of the Trypanosoma cruzi, being modulated by dipeptidyl nitriles and derivatives. Here, four dipeptidyl nitrile derivatives were assayed in three T. cruzi morphologies and two strains (Tulahuen and Y) using a set of assays: (i) analysis of the inhibitory activity against cysteine proteases; (ii) determination of the cytotoxic activity and selectivity index; (iii) verification of the inhibition of the trypomastigote invasion in the host cell. These compounds could inhibit the activity of cysteine proteases using the selective substrate Z-FR-MCA for the trypomastigote lysate and extracellular amastigotes. Interestingly, these compounds did not present relevant enzymatic inhibition for the epimastigote lysate. Most of the substances were also cytotoxic and selective against the trypomastigotes and intracellular amastigotes. The best compound of the series (Neq0662) could reduce the enzymatic activity of the cysteine proteases for the trypomastigotes and amastigotes. It was equipotent to the benznidazole drug in the cytotoxic studies using these two parasite forms. Neq0662 was also selective for the parasite, and it inhibited the invasion of the mammalian host cell in all conditions tested at 10 μM. The stereochemistry of the trifluoromethyl group was an important factor for the bioactivity when the two diastereomers (Neq0662 and Neq0663) were compared. All-in-all, these results indicate that these compounds could move further in the drug development stage because of its promising bioactive profile.
MeSH term(s)	Analysis of Variance ; Animals ; Antiparasitic Agents/chemistry ; Antiparasitic Agents/pharmacology ; Area Under Curve ; Cell Line ; Cell Survival ; Cysteine Proteinase Inhibitors/chemistry ; Cysteine Proteinase Inhibitors/pharmacology ; Cysteine Proteinase Inhibitors/toxicity ; Haplorhini ; Kidney/cytology ; Nitriles/chemistry ; Nitriles/pharmacology ; Proteolysis ; Stereoisomerism ; Tetrazolium Salts ; Thiazoles ; Trypanosoma cruzi/drug effects ; Trypanosoma cruzi/enzymology ; Trypanosoma cruzi/growth & development ; Trypanosoma cruzi/metabolism
Chemical Substances	Antiparasitic Agents ; Cysteine Proteinase Inhibitors ; Nitriles ; Tetrazolium Salts ; Thiazoles ; thiazolyl blue (EUY85H477I)
Language	English
Publishing date	2020-11-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	391089-1
ISSN	1090-2449 ; 0014-4894
ISSN (online)	1090-2449
ISSN	0014-4894
DOI	10.1016/j.exppara.2020.108032
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Article ; Online: Synthesis, biochemical evaluation and molecular modeling studies of nonpeptidic nitrile-based fluorinated compounds.

Fonseca Lameiro, Rafael da / Shamim, Anwar / Rosini, Fabiana / Cendron, Rodrigo / Jatai Batista, Pedro Henrique / Montanari, Carlos Alberto

Future medicinal chemistry

2020 Volume 13, Issue 1, Page(s) 25–43

Abstract: Aim: ...

Abstract	Aim:
MeSH term(s)	Cathepsin L/metabolism ; Chagas Disease/drug therapy ; Cysteine Endopeptidases/metabolism ; Cysteine Proteinase Inhibitors/chemical synthesis ; Cysteine Proteinase Inhibitors/pharmacology ; Drug Discovery ; Fluorine/chemistry ; Humans ; Leishmania mexicana/metabolism ; Leishmaniasis/drug therapy ; Models, Molecular ; Nitriles/chemical synthesis ; Nitriles/pharmacology ; Protozoan Proteins/metabolism ; Structure-Activity Relationship ; Thermodynamics
Chemical Substances	Cysteine Proteinase Inhibitors ; Nitriles ; Protozoan Proteins ; Fluorine (284SYP0193) ; Cysteine Endopeptidases (EC 3.4.22.-) ; endopeptidase B (EC 3.4.22.-) ; Cathepsin L (EC 3.4.22.15) ; cruzipain (EC 3.4.22.51)
Language	English
Publishing date	2020-12-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1756-8927
ISSN (online)	1756-8927
DOI	10.4155/fmc-2020-0057
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Article: Synthesis of a library of glucal-derived triazoles via copper-catalyzed azideâalkyne cyclization

Shamim, Anwar / Frederico B. Souza / HÃ©lio A. Stefani / Stanley N.S. Vasconcelos

Tetrahedron letters. 2017 Mar. 01, v. 58

2017

Abstract: A library of glucal-derived triazoles have been synthesized using the copper-catalyzed azide-alkyne cyclization reaction starting from 3,4,6-tri-O-acetyl-d-glucal. Different trimethylsilyl substituted alkyne derivatives of glucal were first synthesized ... ...

Abstract	A library of glucal-derived triazoles have been synthesized using the copper-catalyzed azide-alkyne cyclization reaction starting from 3,4,6-tri-O-acetyl-d-glucal. Different trimethylsilyl substituted alkyne derivatives of glucal were first synthesized from 3,4,6-tri-O-acetyl-d-glucal, using Sonogashira coupling, hydrostannation and iodination steps. These glucal-based trimethylsilyl-protected alkynes were then used in the copper-catalyzed cyclization reactions with different organic azides to synthesize the corresponding triazole derivatives of d-glucal.
Keywords	alkynes ; azides ; catalysts ; chemical structure ; copper ; iodination ; triazoles
Language	English
Dates of publication	2017-0301
Size	p. 884-888.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	204287-3
ISSN	1873-3581 ; 0040-4039
ISSN (online)	1873-3581
ISSN	0040-4039
DOI	10.1016/j.tetlet.2017.01.059
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Article: Dipeptidyl nitrile derivatives suppress the Trypanosoma cruzi in vitro infection

Quilles, José C / Shamim, Anwar / Tezuka, Daiane Y / Batista, Pedro H.J / Lopes, Carla D / de Albuquerque, Sérgio / Montanari, Carlos A / Leitão, Andrei

Experimental parasitology. 2020 Dec., v. 219

2020

Abstract	Chagas disease affects several countries around the world with health and sanitation problems. Cysteine proteases are essential for the virulence and replication of the Trypanosoma cruzi, being modulated by dipeptidyl nitriles and derivatives. Here, four dipeptidyl nitrile derivatives were assayed in three T. cruzi morphologies and two strains (Tulahuen and Y) using a set of assays: (i) analysis of the inhibitory activity against cysteine proteases; (ii) determination of the cytotoxic activity and selectivity index; (iii) verification of the inhibition of the trypomastigote invasion in the host cell. These compounds could inhibit the activity of cysteine proteases using the selective substrate Z-FR-MCA for the trypomastigote lysate and extracellular amastigotes. Interestingly, these compounds did not present relevant enzymatic inhibition for the epimastigote lysate. Most of the substances were also cytotoxic and selective against the trypomastigotes and intracellular amastigotes. The best compound of the series (Neq0662) could reduce the enzymatic activity of the cysteine proteases for the trypomastigotes and amastigotes. It was equipotent to the benznidazole drug in the cytotoxic studies using these two parasite forms. Neq0662 was also selective for the parasite, and it inhibited the invasion of the mammalian host cell in all conditions tested at 10 μM. The stereochemistry of the trifluoromethyl group was an important factor for the bioactivity when the two diastereomers (Neq0662 and Neq0663) were compared. All-in-all, these results indicate that these compounds could move further in the drug development stage because of its promising bioactive profile.
Keywords	Chagas disease ; Trypanosoma cruzi ; amastigotes ; benznidazole ; cysteine proteinases ; cytotoxicity ; diastereomers ; drug development ; enzyme activity ; enzyme inhibition ; mammals ; nitriles ; parasites ; parasitology ; sanitation ; stereochemistry ; trypomastigotes ; virulence
Language	English
Dates of publication	2020-12
Publishing place	Elsevier Inc.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	391089-1
ISSN	1090-2449 ; 0014-4894
ISSN (online)	1090-2449
ISSN	0014-4894
DOI	10.1016/j.exppara.2020.108032
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Article ; Online: Leaf tissue metabolomics fingerprinting of Citronella gongonha Mart. by

Ali, Sher / Badshah, Gul / Ali, Umar / Siddique Afridi, Muhammad / Shamim, Anwar / Khan, Ajmir / Luiz Felipe Soares, Frederico / Rocha Alencar Menezes, Leociley / Theodoro Rezende, Vanessa / Barison, Andersson / Fernandes de Oliveira, Carlos Augusto / Gustavo Tonin, Fernando

Scientific reports

2022 Volume 12, Issue 1, Page(s) 17624

Abstract: This research characterizes key metabolites in the leaf from Citronella gongonha Martius (Mart.) Howard (Cardiopteridaceae). All metabolites were assessed in intact leaf tissue by proton ( ...

Abstract	This research characterizes key metabolites in the leaf from Citronella gongonha Martius (Mart.) Howard (Cardiopteridaceae). All metabolites were assessed in intact leaf tissue by proton (
MeSH term(s)	Kaempferols/metabolism ; Cymbopogon ; Protons ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Metabolomics/methods ; Magnetic Resonance Spectroscopy/methods ; Plant Leaves/metabolism ; Magnoliopsida ; Monoterpenes/analysis ; Alanine/metabolism ; Sucrose/metabolism ; Glucosides/metabolism
Chemical Substances	Kaempferols ; Protons ; Monoterpenes ; Alanine (OF5P57N2ZX) ; Sucrose (57-50-1) ; Glucosides
Language	English
Publishing date	2022-10-21
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-22708-w
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Article ; Online: Functionalization of protected tyrosine via Sonogashira reaction: synthesis of 3-(1,2,3-triazolyl)-tyrosine.

Vasconcelos, Stanley N S / Shamim, Anwar / Ali, Bakhat / de Oliveira, Isadora M / Stefani, Hélio A

Molecular diversity

2016 Volume 20, Issue 2, Page(s) 469–481

Abstract: 1,2,3-Triazol tyrosines were synthesized from tyrosine alkynes that were in turn prepared via Sonogashira cross-coupling reaction. The tyrosine alkynes were subjected to click-chemistry reaction conditions leading to the corresponding 3-(1,2,3-triazolyl)- ...

Abstract	1,2,3-Triazol tyrosines were synthesized from tyrosine alkynes that were in turn prepared via Sonogashira cross-coupling reaction. The tyrosine alkynes were subjected to click-chemistry reaction conditions leading to the corresponding 3-(1,2,3-triazolyl)-tyrosines in yields ranging from moderate to good.
MeSH term(s)	Alkynes/chemistry ; Catalysis ; Click Chemistry ; Triazoles/chemistry ; Tyrosine/chemical synthesis ; Tyrosine/chemistry
Chemical Substances	Alkynes ; Triazoles ; Tyrosine (42HK56048U)
Language	English
Publishing date	2016-05
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-015-9642-y
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