scholarly journals Structures of plasmepsin X from P. falciparum reveal a novel inactivation mechanism of the zymogen and molecular basis for binding of inhibitors in mature enzyme

2021 ◽  
Author(s):  
pooja kesari ◽  
Anuradha Deshmukh ◽  
Nikhil Pahelkar ◽  
Abhishek B. Suryawanshi ◽  
Ishan Rathore ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Basis ◽  
Drug Target ◽  
Potent Inhibitor ◽  
Malarial Parasite ◽  
Aspartic Proteases ◽  
Apicomplexan Parasites ◽  
Inactivation Mechanism ◽  
Mature Enzyme ◽  
Important Drug

Plasmodium falciparum plasmepsin X (PfPMX), involved in the invasion and egress of this deadliest malarial parasite, is essential for its survival and hence considered as an important drug target. We report the first crystal structure of PfPMX zymogen containing a novel fold of its prosegment. A unique twisted loop from the prosegment and arginine 244 from the mature enzyme are involved in zymogen inactivation; such mechanism, not previously reported, might be common for apicomplexan proteases similar to PfPMX. The maturation of PfPMX zymogen occurs through cleavage of its prosegment at multiple sites. Our data provide thorough insights into the mode of binding of a substrate and a potent inhibitor 49c to PfPMX. We present molecular details of inactivation, maturation, and inhibition of PfPMX that should aid in the development of potent inhibitors against pepsin-like aspartic proteases from apicomplexan parasites.

scholarly journals Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors

Science ◽  
2020 ◽  
Vol 368 (6489) ◽  
pp. 409-412 ◽  
Author(s):  
Linlin Zhang ◽  
Daizong Lin ◽  
Xinyuanyuan Sun ◽  
Ute Curth ◽  
Christian Drosten ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Severe Acute Respiratory Syndrome ◽  
Drug Target ◽  
Essential Role ◽  
Potent Inhibitor ◽  
Amide Bond ◽  
Lead Compound ◽  
X Ray ◽  
Main Protease

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) is a global health emergency. An attractive drug target among coronaviruses is the main protease (Mpro, also called 3CLpro) because of its essential role in processing the polyproteins that are translated from the viral RNA. We report the x-ray structures of the unliganded SARS-CoV-2 Mpro and its complex with an α-ketoamide inhibitor. This was derived from a previously designed inhibitor but with the P3-P2 amide bond incorporated into a pyridone ring to enhance the half-life of the compound in plasma. On the basis of the unliganded structure, we developed the lead compound into a potent inhibitor of the SARS-CoV-2 Mpro. The pharmacokinetic characterization of the optimized inhibitor reveals a pronounced lung tropism and suitability for administration by the inhalative route.

scholarly journals Divergent features of the coenzyme Q:cytochrome c oxidoreductase complex in Toxoplasma gondii parasites

2021 ◽  
Vol 17 (2) ◽  
pp. e1009211
Author(s):  
Jenni A. Hayward ◽  
Esther Rajendran ◽  
Soraya M. Zwahlen ◽  
Pierre Faou ◽  
Giel G. van Dooren
Keyword(s):  
Toxoplasma Gondii ◽  
Drug Target ◽  
Protein Composition ◽  
Complex Iii ◽  
Mitochondrial Electron Transport Chain ◽  
Eukaryotic Evolution ◽  
Mitochondrial Oxygen Consumption ◽  
Apicomplexan Parasites ◽  
Transport Chain ◽  
Important Drug

The mitochondrion is critical for the survival of apicomplexan parasites. Several major anti-parasitic drugs, such as atovaquone and endochin-like quinolones, act through inhibition of the mitochondrial electron transport chain at the coenzyme Q:cytochrome c oxidoreductase complex (Complex III). Despite being an important drug target, the protein composition of Complex III of apicomplexan parasites has not been elucidated. Here, we undertake a mass spectrometry-based proteomic analysis of Complex III in the apicomplexan Toxoplasma gondii. Along with canonical subunits that are conserved across eukaryotic evolution, we identify several novel or highly divergent Complex III components that are conserved within the apicomplexan lineage. We demonstrate that one such subunit, which we term TgQCR11, is critical for parasite proliferation, mitochondrial oxygen consumption and Complex III activity, and establish that loss of this protein leads to defects in Complex III integrity. We conclude that the protein composition of Complex III in apicomplexans differs from that of the mammalian hosts that these parasites infect.

The X-ray structure ofSalmonella typhimuriumuridine nucleoside phosphorylase complexed with 2,2′-anhydrouridine, phosphate and potassium ions at 1.86 Å resolution

2009 ◽  
Vol 66 (1) ◽  
pp. 51-60 ◽  
Author(s):  
Alexander A. Lashkov ◽  
Nadezhda E. Zhukhlistova ◽  
Azat H. Gabdoulkhakov ◽  
Alexander A. Shtil ◽  
Roman G. Efremov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Salmonella Typhimurium ◽  
Drug Target ◽  
Computational Approach ◽  
Potassium Ions ◽  
Uridine Phosphorylase ◽  
Nucleoside Phosphorylase ◽  
X Ray ◽  
Antitumour Agents ◽  
Important Drug

Uridine nucleoside phosphorylase is an important drug target for the development of anti-infective and antitumour agents. The X-ray crystal structure ofSalmonella typhimuriumuridine nucleoside phosphorylase (StUPh) complexed with its inhibitor 2,2′-anhydrouridine, phosphate and potassium ions has been solved and refined at 1.86 Å resolution (Rcryst= 17.6%,Rfree= 20.6%). The complex of human uridine phosphorylase I (HUPhI) with 2,2′-anhydrouridine was modelled using a computational approach. The model allowed the identification of atomic groups in 2,2′-anhydrouridine that might improve the interaction of future inhibitors withStUPh andHUPhI.

Memapsin 2, a drug target for Alzheimer's disease

2003 ◽  
Vol 70 ◽  
pp. 213-220 ◽  
Author(s):  
Gerald Koelsch ◽  
Robert T. Turner ◽  
Lin Hong ◽  
Arun K. Ghosh ◽  
Jordan Tang
Keyword(s):  
Crystal Structure ◽  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Transition State ◽  
Amyloid Precursor Protein ◽  
Therapeutic Target ◽  
Drug Target ◽  
Aspartic Protease ◽  
Precursor Protein ◽  
Memapsin 2

Mempasin 2, a ϐ-secretase, is the membrane-anchored aspartic protease that initiates the cleavage of amyloid precursor protein leading to the production of ϐ-amyloid and the onset of Alzheimer's disease. Thus memapsin 2 is a major therapeutic target for the development of inhibitor drugs for the disease. Many biochemical tools, such as the specificity and crystal structure, have been established and have led to the design of potent and relatively small transition-state inhibitors. Although developing a clinically viable mempasin 2 inhibitor remains challenging, progress to date renders hope that memapsin 2 inhibitors may ultimately be useful for therapeutic reduction of ϐ-amyloid.

scholarly journals Structural analysis of human dual-specificity phosphatase 22 complexed with a phosphotyrosine-like substrate

2015 ◽  
Vol 71 (2) ◽  
pp. 199-205 ◽  
Author(s):  
George T. Lountos ◽  
Scott Cherry ◽  
Joseph E. Tropea ◽  
David S. Waugh
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Phosphatase Activity ◽  
Small Molecule ◽  
Molecular Basis ◽  
Protein Tyrosine Phosphatases ◽  
Simple Method ◽  
Dual Specificity Phosphatase ◽  
Dual Specificity ◽  
Nitrophenyl Phosphate

4-Nitrophenyl phosphate (p-nitrophenyl phosphate, pNPP) is widely used as a small molecule phosphotyrosine-like substrate in activity assays for protein tyrosine phosphatases. It is a colorless substrate that upon hydrolysis is converted to a yellow 4-nitrophenolate ion that can be monitored by absorbance at 405 nm. Therefore, the pNPP assay has been widely adopted as a quick and simple method to assess phosphatase activity and is also commonly used in assays to screen for inhibitors. Here, the first crystal structure is presented of a dual-specificity phosphatase, human dual-specificity phosphatase 22 (DUSP22), in complex with pNPP. The structure illuminates the molecular basis for substrate binding and may also facilitate the structure-assisted development of DUSP22 inhibitors.

The Crystal Structure of the C-Terminal DAP5/p97 Domain Sheds Light on the Molecular Basis for Its Processing by Caspase Cleavage

2008 ◽  
Vol 383 (3) ◽  
pp. 539-548 ◽  
Author(s):  
Noa Liberman ◽  
Orly Dym ◽  
Tamar Unger ◽  
Shira Albeck ◽  
Yoav Peleg ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Basis ◽  
Caspase Cleavage

scholarly journals The structure of the metallo-β-lactamase VIM-2 in complex with a triazolylthioacetamide inhibitor

2016 ◽  
Vol 72 (11) ◽  
pp. 813-819 ◽  
Author(s):  
Tony Christopeit ◽  
Ke-Wu Yang ◽  
Shao-Kang Yang ◽  
Hanna-Kirsti S. Leiros
Keyword(s):  
Public Health ◽  
Crystal Structure ◽  
Active Site ◽  
Drug Target ◽  
Zinc Ions ◽  
Clinical Use ◽  
Global Public Health ◽  
Promising Strategy ◽  
Conserved Residue ◽  
Substrate Spectrum

The increasing number of pathogens expressing metallo-β-lactamases (MBLs), and in this way achieving resistance to β-lactam antibiotics, is a significant threat to global public health. A promising strategy to treat such resistant pathogens is the co-administration of MBL inhibitors together with β-lactam antibiotics. However, an MBL inhibitor suitable for clinical use has not yet been identified. Verona integron-encoded metallo-β-lactamase 2 (VIM-2) is a widespread MBL with a broad substrate spectrum and hence is an interesting drug target for the treatment of β-lactam-resistant infections. In this study, three triazolylthioacetamides were tested as inhibitors of VIM-2. One of the tested compounds showed clear inhibition of VIM-2, with an IC50of 20 µM. The crystal structure of the inhibitor in complex with VIM-2 was obtained by DMSO-free co-crystallization and was solved at a resolution of 1.50 Å. To our knowledge, this is the first structure of a triazolylthioacetamide inhibitor in complex with an MBL. Analysis of the structure shows that the inhibitor binds to the two zinc ions in the active site of VIM-2 and revealed detailed information on the interactions involved. Furthermore, the crystal structure showed that binding of the inhibitor induced a conformational change of the conserved residue Trp87.

scholarly journals Effects of Atovaquone and Diospyrin-Based Drugs on the Cellular ATP of Pneumocystis carinii f. sp.carinii

2000 ◽  
Vol 44 (3) ◽  
pp. 713-719 ◽  
Author(s):  
Melanie T. Cushion ◽  
Margaret Collins ◽  
Banasri Hazra ◽  
Edna S. Kaneshiro
Keyword(s):  
Electron Transport ◽  
Drug Target ◽  
Coenzyme Q ◽  
Pneumocystis Carinii ◽  
Atp Depletion ◽  
Malarial Parasite ◽  
Dihydroorotate Dehydrogenase ◽  
Atp Levels ◽  
Transport Chain ◽  
Kinetics Of

ABSTRACT Atovaquone (also called Mepron, or 566C80) is a napthoquinone used for the treatment of infections caused by pathogens such asPlasmodium spp. and Pneumocystis carinii. The mechanism of action against the malarial parasite is the inhibition of dihydroorotate dehydrogenase (DHOD), a consequence of blocking electron transport by the drug. As an analog of ubiquinone (coenzyme Q [CoQ]), atovaquone irreversibly binds to the mitochondrial cytochrome bc 1 complex; thus, electrons are not able to pass from dehydrogenase enzymes via CoQ to cytochrome c. Since DHOD is a critical enzyme in pyrimidine biosynthesis, and because the parasite cannot scavenge host pyrimidines, the drug is lethal to the organism. Oxygen consumption inP. carinii is inhibited by the drug; thus, electron transport has also been identified as the drug target in P. carinii. However, unlike Plasmodium DHOD, P. carinii DHOD is inhibited only at high atovaquone concentrations, suggesting that the organism may salvage host pyrimidines and that atovaquone exerts its primary effects on ATP biosynthesis. In the present study, the effect of atovaquone on ATP levels in P. carinii was measured directly from 1 to 6 h and then after 24, 48, and 72 h of exposure. The average 50% inhibitory concentration after 24 to 72 h of exposure was 1.5 μg/ml (4.2 μM). The kinetics of ATP depletion were in contrast to those of another family of naphthoquinone compounds, diospyrin and two of its derivatives. Whereas atovaquone reduced ATP levels within 1 h of exposure, the diospyrins required at least 48 h. After 72 h, the diospyrins were able to decrease ATP levels of P. carinii at nanomolar concentrations. These data indicate that although naphthoquinones inhibit the electron transport chain, the molecular targets in a given organism are likely to be distinct among members of this class of compounds.

scholarly journals Crystal structure of SARS-CoV-2 main protease in complex with a Chinese herb inhibitor shikonin

2020 ◽  
Author(s):  
Jian Li ◽  
Xuelan Zhou ◽  
Yan Zhang ◽  
Fanglin Zhong ◽  
Cheng Lin ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Drug Targets ◽  
Chinese Herb ◽  
Binding Modes ◽  
High Potency ◽  
Main Protease ◽  
Covalent Inhibitors ◽  
Catalytic Dyad ◽  
Important Drug

AbstractMain protease (Mpro, also known as 3CLpro) has a major role in the replication of coronavirus life cycle and is one of the most important drug targets for anticoronavirus agents. Here we report the crystal structure of main protease of SARS-CoV-2 bound to a previously identified Chinese herb inhibitor shikonin at 2.45 angstrom resolution. Although the structure revealed here shares similar overall structure with other published structures, there are several key differences which highlight potential features that could be exploited. The catalytic dyad His41-Cys145 undergoes dramatic conformational changes, and the structure reveals an unusual arrangement of oxyanion loop stabilized by the substrate. Binding to shikonin and binding of covalent inhibitors show different binding modes, suggesting a diversity in inhibitor binding. As we learn more about different binding modes and their structure-function relationships, it is probable that we can design more effective and specific drugs with high potency that can serve as effect SARS-CoV-2 anti-viral agents.

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