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Goettig P, Chen X, Harris JM. Correlation of Experimental and Calculated Inhibition Constants of Protease Inhibitor Complexes. Int J Mol Sci 2024; 25:2429. [PMID: 38397107 PMCID: PMC10889394 DOI: 10.3390/ijms25042429] [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: 12/14/2023] [Revised: 01/28/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Predicting the potency of inhibitors is key to in silico screening of promising synthetic or natural compounds. Here we describe a predictive workflow that provides calculated inhibitory values, which concord well with empirical data. Calculations of the free interaction energy ΔG with the YASARA plugin FoldX were used to derive inhibition constants Ki from PDB coordinates of protease-inhibitor complexes. At the same time, corresponding KD values were obtained from the PRODIGY server. These results correlated well with the experimental values, particularly for serine proteases. In addition, analyses were performed for inhibitory complexes of cysteine and aspartic proteases, as well as of metalloproteases, whereby the PRODIGY data appeared to be more consistent. Based on our analyses, we calculated theoretical Ki values for trypsin with sunflower trypsin inhibitor (SFTI-1) variants, which yielded the more rigid Pro14 variant, with probably higher potency than the wild-type inhibitor. Moreover, a hirudin variant with an Arg1 and Trp3 is a promising basis for novel thrombin inhibitors with high potency. Further examples from antibody interaction and a cancer-related effector-receptor system demonstrate that our approach is applicable to protein interaction studies beyond the protease field.
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Affiliation(s)
- Peter Goettig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia or (X.C.); (J.M.H.)
| | - Xingchen Chen
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia or (X.C.); (J.M.H.)
| | - Jonathan M. Harris
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia or (X.C.); (J.M.H.)
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2
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Hulme J. COVID-19 and Diarylamidines: The Parasitic Connection. Int J Mol Sci 2023; 24:6583. [PMID: 37047556 PMCID: PMC10094973 DOI: 10.3390/ijms24076583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
As emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants (Omicron) continue to outpace and negate combinatorial vaccines and monoclonal antibody therapies targeting the spike protein (S) receptor binding domain (RBD), the appetite for developing similar COVID-19 treatments has significantly diminished, with the attention of the scientific community switching to long COVID treatments. However, treatments that reduce the risk of "post-COVID-19 syndrome" and associated sequelae remain in their infancy, particularly as no established criteria for diagnosis currently exist. Thus, alternative therapies that reduce infection and prevent the broad range of symptoms associated with 'post-COVID-19 syndrome' require investigation. This review begins with an overview of the parasitic-diarylamidine connection, followed by the renin-angiotensin system (RAS) and associated angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSSR2) involved in SARS-CoV-2 infection. Subsequently, the ability of diarylamidines to inhibit S-protein binding and various membrane serine proteases associated with SARS-CoV-2 and parasitic infections are discussed. Finally, the roles of diarylamidines (primarily DIZE) in vaccine efficacy, epigenetics, and the potential amelioration of long COVID sequelae are highlighted.
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Affiliation(s)
- John Hulme
- Department of Bionano Technology, Gachon Bionano Research Institute, Gachon University, 1342 Sungnam-daero, Sujung-gu, Seongnam-si 461-701, Republic of Korea
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3
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Nakamura S, Akaki T, Nishiwaki K, Nakatani M, Kawase Y, Takahashi Y, Nakanishi I. System truncation accelerates binding affinity calculations with the fragment molecular orbital method: A benchmark study. J Comput Chem 2023; 44:824-831. [PMID: 36444861 DOI: 10.1002/jcc.27044] [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: 08/07/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022]
Abstract
The fragment molecular orbital (FMO) method is a fast quantum-mechanical method that divides systems into pieces of fragments and performs ab initio calculations. The system truncation enables further speed improvement. In this article, we systematically study the effects of system truncations on binding affinity calculations obtained with FMO in combination with either the polarizable continuum model (FMO/PCM) or in combination with the Møller-Plesset method (FMO-MP2). We have used five protein complexes with ligands of several charged states. The calculated binding energies of the size variants of the truncated system, including only a restricted number of atoms around the ligand, are compared to the energy obtained from a full system. The result shows that the systems could be truncated to a radius of 8 Å from neutral ligands within an error of 0.7 kcal/mol, and 12 Å from charged ligands within an error of 1.1 kcal/mol for calculating the binding energy in solution.
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Affiliation(s)
- Shinya Nakamura
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Tatsuo Akaki
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan.,Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, Japan
| | - Keiji Nishiwaki
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Midori Nakatani
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Yuji Kawase
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Yuki Takahashi
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
| | - Isao Nakanishi
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan
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4
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Mehner C, Hockla A, Coban M, Madden B, Estrada R, Radisky DC, Radisky ES. Activity-based protein profiling reveals active serine proteases that drive malignancy of human ovarian clear cell carcinoma. J Biol Chem 2022; 298:102146. [PMID: 35716777 PMCID: PMC9304776 DOI: 10.1016/j.jbc.2022.102146] [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: 12/15/2021] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 12/14/2022] Open
Abstract
Ovarian clear cell carcinoma (OCCC) is an understudied poor prognosis subtype of ovarian cancer lacking in effective targeted therapies. Efforts to define molecular drivers of OCCC malignancy may lead to new therapeutic targets and approaches. Among potential targets are secreted proteases, enzymes which in many cancers serve as key drivers of malignant progression. Here, we found that inhibitors of trypsin-like serine proteases suppressed malignant phenotypes of OCCC cell lines. To identify the proteases responsible for malignancy in OCCC, we employed activity-based protein profiling to directly analyze enzyme activity. We developed an activity-based probe featuring an arginine diphenylphosphonate warhead to detect active serine proteases of trypsin-like specificity and a biotin handle to facilitate affinity purification of labeled proteases. Using this probe, we identified active trypsin-like serine proteases within the complex proteomes secreted by OCCC cell lines, including two proteases in common, tissue plasminogen activator and urokinase-type plasminogen activator. Further interrogation of these proteases showed that both were involved in cancer cell invasion and proliferation of OCCC cells and were also detected in in vivo models of OCCC. We conclude the detection of tissue plasminogen activator and urokinase-type plasminogen activator as catalytically active proteases and significant drivers of the malignant phenotype may point to these enzymes as targets for new therapeutic strategies in OCCC. Our activity-based probe and profiling methodology will also serve as a valuable tool for detection of active trypsin-like serine proteases in models of other cancers and other diseases.
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Affiliation(s)
- Christine Mehner
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota, USA,Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Alexandra Hockla
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Mathew Coban
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Benjamin Madden
- Medical Genome Facility Proteomics Core, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Derek C. Radisky
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Evette S. Radisky
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA,For correspondence: Evette S. Radisky
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5
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Sanderson L, da Silva M, Sekhar GN, Brown RC, Burrell-Saward H, Fidanboylu M, Liu B, Dailey LA, Dreiss CA, Lorenz C, Christie M, Persaud SJ, Yardley V, Croft SL, Valero M, Thomas SA. Drug reformulation for a neglected disease. The NANOHAT project to develop a safer more effective sleeping sickness drug. PLoS Negl Trop Dis 2021; 15:e0009276. [PMID: 33857146 PMCID: PMC8078842 DOI: 10.1371/journal.pntd.0009276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/27/2021] [Accepted: 02/26/2021] [Indexed: 01/16/2023] Open
Abstract
Background Human African trypanosomiasis (HAT or sleeping sickness) is caused by the
parasite Trypanosoma brucei sspp. The disease has two
stages, a haemolymphatic stage after the bite of an infected tsetse fly,
followed by a central nervous system stage where the parasite penetrates the
brain, causing death if untreated. Treatment is stage-specific, due to the
blood-brain barrier, with less toxic drugs such as pentamidine used to treat
stage 1. The objective of our research programme was to develop an
intravenous formulation of pentamidine which increases CNS exposure by some
10–100 fold, leading to efficacy against a model of stage 2 HAT. This target
candidate profile is in line with drugs for neglected diseases inititative
recommendations. Methodology To do this, we evaluated the physicochemical and structural characteristics
of formulations of pentamidine with Pluronic micelles (triblock-copolymers
of polyethylene-oxide and polypropylene oxide), selected candidates for
efficacy and toxicity evaluation in vitro, quantified
pentamidine CNS delivery of a sub-set of formulations in vitro and
in vivo, and progressed one pentamidine-Pluronic formulation
for further evaluation using an in vivo single dose brain
penetration study. Principal Findings Screening pentamidine against 40 CNS targets did not reveal any major
neurotoxicity concerns, however, pentamidine had a high affinity for the
imidazoline2 receptor. The reduction in insulin secretion in
MIN6 β-cells by pentamidine may be secondary to pentamidine-mediated
activation of β-cell imidazoline receptors and impairment of cell viability.
Pluronic F68 (0.01%w/v)-pentamidine formulation had a similar inhibitory
effect on insulin secretion as pentamidine alone and an additive
trypanocidal effect in vitro. However, all Pluronics tested
(P85, P105 and F68) did not significantly enhance brain exposure of
pentamidine. Significance These results are relevant to further developing block-copolymers as
nanocarriers, improving BBB drug penetration and understanding the side
effects of pentamidine. Sleeping sickness or human African Trypanosomiasis (HAT) is a disease caused by a
parasite, which is transferred to humans by the bite of an infected tsetse fly.
There are two disease stages: the first stage is the blood-based stage of the
disease and the second stage affects the brain. It is fatal if left untreated.
The blood-brain barrier (BBB) makes the brain stage difficult to treat because
it prevents 99% of all drugs from entering the brain from the blood. Those
anti-HAT drugs that do enter the brain are toxic and have serious side effects.
Pentamidine is a less toxic blood stage drug, which our research has shown has a
limited ability to cross the BBB due to its removal by proteins called
transporters. The objective of this study was to use Pluronic to improve
pentamidine delivery to target sites, whilst reducing its side effects. Pluronic
is a polymer, which can assemble into micelles and encapsulate the drug. Thus,
prolonging its circulation time and protecting it. Our study indicated that the
selected Pluronics did not increase the brain delivery of pentamidine. However.
Pluronic-pentamidine formulations were identified that harboured trypanocidal
activity and did not increase safety concerns compared to unformulated
pentamidine.
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Affiliation(s)
- Lisa Sanderson
- King’s College London, Institute of Pharmaceutical Science,
Franklin-Wilkins Building, Stamford Street, London, United
Kingdom
| | - Marcelo da Silva
- King’s College London, Institute of Pharmaceutical Science,
Franklin-Wilkins Building, Stamford Street, London, United
Kingdom
| | - Gayathri N. Sekhar
- King’s College London, Institute of Pharmaceutical Science,
Franklin-Wilkins Building, Stamford Street, London, United
Kingdom
| | - Rachel C. Brown
- King’s College London, Institute of Pharmaceutical Science,
Franklin-Wilkins Building, Stamford Street, London, United
Kingdom
| | - Hollie Burrell-Saward
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and
Tropical Medicine, London, United Kingdom
| | - Mehmet Fidanboylu
- King’s College London, Institute of Pharmaceutical Science,
Franklin-Wilkins Building, Stamford Street, London, United
Kingdom
| | - Bo Liu
- King’s College London, Department of Diabetes, School of Life Course
Sciences, Faculty of Life Sciences & Medicine, London, United
Kingdom
| | - Lea Ann Dailey
- King’s College London, Institute of Pharmaceutical Science,
Franklin-Wilkins Building, Stamford Street, London, United
Kingdom
| | - Cécile A. Dreiss
- King’s College London, Institute of Pharmaceutical Science,
Franklin-Wilkins Building, Stamford Street, London, United
Kingdom
| | - Chris Lorenz
- King’s College London, Theory & Simulation of Condensed Matter Group,
Department of Physics, Strand, London, United Kingdom
| | - Mark Christie
- King’s College London, Institute of Pharmaceutical Science,
Franklin-Wilkins Building, Stamford Street, London, United
Kingdom
| | - Shanta J. Persaud
- King’s College London, Department of Diabetes, School of Life Course
Sciences, Faculty of Life Sciences & Medicine, London, United
Kingdom
| | - Vanessa Yardley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and
Tropical Medicine, London, United Kingdom
| | - Simon L. Croft
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and
Tropical Medicine, London, United Kingdom
| | - Margarita Valero
- Physical Chemistry Department, Faculty of Pharmacy, University of
Salamanca, Salamanca, Spain
| | - Sarah A. Thomas
- King’s College London, Institute of Pharmaceutical Science,
Franklin-Wilkins Building, Stamford Street, London, United
Kingdom
- * E-mail:
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6
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Patel N, Arfeen M, Singh T, Bhagat S, Sakhare A, Bharatam PV. Divalent N I Compounds: Identifying new Carbocyclic Carbenes to Design Nitreones using Quantum Chemical Methods. J Comput Chem 2020; 41:2624-2633. [PMID: 32964506 DOI: 10.1002/jcc.26417] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/23/2020] [Accepted: 08/24/2020] [Indexed: 11/05/2022]
Abstract
Nitreones are compounds with oxidation state 1 at the nitrogen, these compounds carry formal positive charge as well as two lone pairs of electrons at nitrogen center. These compounds are also known as divalent NI compounds and can be represented with the general formula L → N+ ← L, where L is an electron donating ligand. In the recent past, several divalent NI compounds have been reported with L = N-heterocyclic carbene (NHC), remote N-heterocyclic carbene (rNHC), carbocyclic carbene (CCC) and diaminocarbene. Recently, our group reported that a novel six-membered CCC (cyclohexa-2,5-diene-4-[diaminomethynyl]-1-ylidene) can stabilize N+ center in nitreones. As an independent carbene, this species is very unstable. In this work, modulation of this CCC using (a) annulation, (b) heterocyclic ring modification, (c) substitutions adjacent to the carbenic carbon, (d) exocyclic double bond insertion and (e) ring contraction, has been reported. These modulations and quantum chemical analyses helped in the identification of five new six-membered CCCs which carry improved donation and stability properties. Further, these CCCs were employed in the design of new divalent NI compounds (nitreones) which carry coordination bonds between ligands and N+ center. The molecular and electronic structure properties, and the donor→acceptor coordination interactions present in the resultant low oxidation state divalent NI compounds have been explored.
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Affiliation(s)
- Neha Patel
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S. A. S. Nagar, Punjab, India
- Biocon Bristol-Myers Squibb R&D Center (BBRC), Syngene International Ltd., Bengaluru, Karnataka, India
| | - Minhajul Arfeen
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S. A. S. Nagar, Punjab, India
| | - Tejender Singh
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S. A. S. Nagar, Punjab, India
| | - Shweta Bhagat
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S. A. S. Nagar, Punjab, India
| | - Ajay Sakhare
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S. A. S. Nagar, Punjab, India
| | - Prasad V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S. A. S. Nagar, Punjab, India
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7
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Manohar R, Kutumbarao NHV, Krishna Nagampalli RS, Velmurugan D, Gunasekaran K. Structural insights and binding of a natural ligand, succinic acid with serine and cysteine proteases. Biochem Biophys Res Commun 2017; 495:679-685. [PMID: 29127014 DOI: 10.1016/j.bbrc.2017.11.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 11/05/2017] [Indexed: 01/01/2023]
Abstract
In the age of growing infectious diseases, there is a great demand for new inhibitors which can exhibit minimum side effects. Owing to the importance of proteases in life cycle and invasion, they have been projected as attractive targets for structure based drug designing against microbes including viruses. Here we report the inhibitory activity of a well known natural compound succinic acid against both serine and cysteine proteases. The ligand is found co-crystallized with Bovine pancreatic trypsin in one of our crystallization trials and the diffraction data up to1.9 Å reveal its interactions with the catalytic triad residues Histidine 57 and Serine 195. Binding of the ligand with these proteases have been validated using caseinolysis inhibition. With trypsin, ITC analysis showed tight binding of the ligand, resulting in change in Gibb's free energy (ΔG) by -20.31 kJ/mol. To understand the existence of succinic acid at the active site, molecular docking was performed and it revealed binding of it with trypsin and papain at corresponding active sites. This dual inhibitory activity of natural ligand, succinic acid can be accounted for the recent reports on anti-viral property of plant extracts where dicarboxilic fatty acids are normally abundant.
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Affiliation(s)
- R Manohar
- CAS in Crystallography and Biophysics, University of Madras, Chennai 600025, India
| | - N H V Kutumbarao
- CAS in Crystallography and Biophysics, University of Madras, Chennai 600025, India
| | | | - D Velmurugan
- CAS in Crystallography and Biophysics, University of Madras, Chennai 600025, India
| | - K Gunasekaran
- CAS in Crystallography and Biophysics, University of Madras, Chennai 600025, India.
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8
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Grille Coronel L, Acierno JP, Ermácora MR. Ultracompact states of native proteins. Biophys Chem 2017; 230:36-44. [DOI: 10.1016/j.bpc.2017.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 08/16/2017] [Indexed: 10/19/2022]
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9
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Grimmelsmann L, Marefat Khah A, Spies C, Hättig C, Nuernberger P. Ultrafast Dynamics of a Triazene: Excited-State Pathways and the Impact of Binding to the Minor Groove of DNA and Further Biomolecular Systems. J Phys Chem Lett 2017; 8:1986-1992. [PMID: 28426228 DOI: 10.1021/acs.jpclett.7b00472] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Many synthetic DNA minor groove binders exhibit a strong increase in fluorescence when bound to DNA. The pharmaceutical-relevant berenil (diminazene aceturate) is an exception with an extremely low fluorescence quantum yield (on the order of 10-4). We investigate the ultrafast excited-state dynamics of this triazene by femtosecond time-resolved fluorescence experiments in water, ethylene glycol, and buffer and bound to the enzyme β-trypsin, the minor groove of AT-rich DNA, and G-quadruplex DNA. Ab initio calculations provide additional mechanistic insight. The complementing studies unveil that the excited-state motion initiated by ππ* excitation occurs in two phases: a subpicosecond phase associated with the lengthening of the central N═N double bond, followed by a bicycle-pedal-type motion of the triazene bridge, which is almost volume-conserving and can proceed efficiently within only a few picoseconds even under spatially confined conditions. Our results elucidate the excited-state relaxation mechanism of aromatic triazenes and explain the modest sensitivity of the fluorescence quantum yield of berenil even when it is bound to various biomolecules.
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Affiliation(s)
- Lena Grimmelsmann
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
| | - Alireza Marefat Khah
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
| | - Christian Spies
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
| | - Christof Hättig
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
| | - Patrick Nuernberger
- Physikalische Chemie II and ‡Theoretische Chemie, Ruhr-Universität Bochum , 44780 Bochum, Germany
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10
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Kayode O, Huang Z, Soares AS, Caulfield TR, Dong Z, Bode AM, Radisky ES. Small molecule inhibitors of mesotrypsin from a structure-based docking screen. PLoS One 2017; 12:e0176694. [PMID: 28463992 PMCID: PMC5413004 DOI: 10.1371/journal.pone.0176694] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/16/2017] [Indexed: 01/18/2023] Open
Abstract
PRSS3/mesotrypsin is an atypical isoform of trypsin, the upregulation of which has been implicated in promoting tumor progression. To date there are no mesotrypsin-selective pharmacological inhibitors which could serve as tools for deciphering the pathological role of this enzyme, and could potentially form the basis for novel therapeutic strategies targeting mesotrypsin. A virtual screen of the Natural Product Database (NPD) and Food and Drug Administration (FDA) approved Drug Database was conducted by high-throughput molecular docking utilizing crystal structures of mesotrypsin. Twelve high-scoring compounds were selected for testing based on lowest free energy docking scores, interaction with key mesotrypsin active site residues, and commercial availability. Diminazene (CID22956468), along with two similar compounds presenting the bis-benzamidine substructure, was validated as a competitive inhibitor of mesotrypsin and other human trypsin isoforms. Diminazene is the most potent small molecule inhibitor of mesotrypsin reported to date with an inhibitory constant (Ki) of 3.6±0.3 μM. Diminazene was subsequently co-crystalized with mesotrypsin and the crystal structure was solved and refined to 1.25 Å resolution. This high resolution crystal structure can now offer a foundation for structure-guided efforts to develop novel and potentially more selective mesotrypsin inhibitors based on similar molecular substructures.
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Affiliation(s)
- Olumide Kayode
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, United States of America
| | - Zunnan Huang
- The Hormel Institute, University of Minnesota, Austin, Minnesota, United States of America
| | - Alexei S. Soares
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Thomas R. Caulfield
- Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, Florida, United States of America
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, Austin, Minnesota, United States of America
| | - Ann M. Bode
- The Hormel Institute, University of Minnesota, Austin, Minnesota, United States of America
| | - Evette S. Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, United States of America
- * E-mail:
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11
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Wu SY, Park GY, Kim SH, Hulme J, An SSA. Diminazene aceturate: an antibacterial agent for Shiga-toxin-producing Escherichia coli O157:H7. DRUG DESIGN DEVELOPMENT AND THERAPY 2016; 10:3363-3378. [PMID: 27789937 PMCID: PMC5072558 DOI: 10.2147/dddt.s114832] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The aim of this study was to investigate the bacteriostatic and bactericidal effects of diminazene aceturate (DA) against five strains of pathogenic bacteria and two strains of nonpathogenic bacteria. The results showed that 5 μg/mL of DA suppressed the growth of pathogenic Escherichia coli by as much as 77% compared with the controls. Enterohemorrhagic E. coli EDL933 (an E. coli O157:H7 strain) was the most sensitive to DA with a minimum inhibitory concentration of 20 μg/mL. Additional investigations showed that DA induced the highest level of intracellular reactive oxygen species in EDL933. A positive correlation between the reactive oxygen species levels and DA concentration was demonstrated. DA (5 μg/mL) was also a potent uncoupler, inducing a stationary phase collapse (70%–75%) in both strains of E. coli O157:H7. Further investigation showed that the collapse was due to the NaCl:DA ratio in the broth and was potassium ion dependent. A protease screening assay was conducted to elucidate the underlying mechanism. It was found that at neutral pH, the hydrolysis of H-Asp-pNA increased by a factor of 2–3 in the presence of DA, implying that DA causes dysregulation of the proton motive force and a decrease in cellular pH. Finally, a commercial verotoxin test showed that DA did not significantly increase toxin production in EDL933 and was a suitable antibacterial agent for Shiga-toxin-producing E. coli.
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Affiliation(s)
- Si-Ying Wu
- Department of BioNano Technology, Gachon BioNano Research Institute, Gachon University, Seongnam-si
| | - Gil-Yong Park
- Department of BioNano Technology, Gachon BioNano Research Institute, Gachon University, Seongnam-si
| | - So-Hee Kim
- Seoul National University Bundang Hospital, Gyeonggi-do, Republic of Korea
| | - John Hulme
- Department of BioNano Technology, Gachon BioNano Research Institute, Gachon University, Seongnam-si
| | - Seong Soo A An
- Department of BioNano Technology, Gachon BioNano Research Institute, Gachon University, Seongnam-si
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12
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Risso VA, Acierno JP, Capaldi S, Monaco HL, Ermácora MR. X-ray evidence of a native state with increased compactness populated by tryptophan-less B. licheniformis β-lactamase. Protein Sci 2012; 21:964-76. [PMID: 22496053 DOI: 10.1002/pro.2076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 03/25/2012] [Accepted: 03/29/2012] [Indexed: 11/12/2022]
Abstract
β-lactamases confer antibiotic resistance, one of the most serious world-wide health problems, and are an excellent theoretical and experimental model in the study of protein structure, dynamics and evolution. Bacillus licheniformis exo-small penicillinase (ESP) is a Class-A β-lactamase with three tryptophan residues located in the protein core. Here, we report the 1.7-Å resolution X-ray structure, catalytic parameters, and thermodynamic stability of ESP(ΔW), an engineered mutant of ESP in which phenylalanine replaces the wild-type tryptophan residues. The structure revealed no qualitative conformational changes compared with thirteen previously reported structures of B. licheniformis β-lactamases (RMSD = 0.4-1.2 Å). However, a closer scrutiny showed that the mutations result in an overall more compact structure, with most atoms shifted toward the geometric center of the molecule. Thus, ESP(ΔW) has a significantly smaller radius of gyration (R(g)) than the other B. licheniformis β-lactamases characterized so far. Indeed, ESP(ΔW) has the smallest R(g) among 126 Class-A β-lactamases in the Protein Data Bank (PDB). Other measures of compactness, like the number of atoms in fixed volumes and the number and average of noncovalent distances, confirmed the effect. ESP(ΔW) proves that the compactness of the native state can be enhanced by protein engineering and establishes a new lower limit to the compactness of the Class-A β-lactamase fold. As the condensation achieved by the native state is a paramount notion in protein folding, this result may contribute to a better understanding of how the sequence determines the conformational variability and thermodynamic stability of a given fold.
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Affiliation(s)
- Valeria A Risso
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 325, 1876 Bernal, Buenos Aires, Argentina
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Surpateanu G, Iorga BI. Evaluation of docking performance in a blinded virtual screening of fragment-like trypsin inhibitors. J Comput Aided Mol Des 2011; 26:595-601. [DOI: 10.1007/s10822-011-9526-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Accepted: 12/08/2011] [Indexed: 10/14/2022]
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14
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Fuchs JE, Spitzer GM, Javed A, Biela A, Kreutz C, Wellenzohn B, Liedl KR. Minor groove binders and drugs targeting proteins cover complementary regions in chemical shape space. J Chem Inf Model 2011; 51:2223-32. [PMID: 21819135 DOI: 10.1021/ci200237c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA minor groove binders (MGBs) are known to influence gene expression and are therefore widely studied to explore their therapeutic potential. We identified shape-based virtual screening with ROCS as a highly effective computational approach to enrich known MGBs in top-ranked molecules. Discovery of ten previously unknown MGBs by shape-based screening further confirmed the relevance of ligand shape for minor groove affinity. Based on experimental testing we propose three simple rules (at least two positive charges, four nitrogen atoms, and one aromatic ring) as filters to reach even better enrichment of true positives in ROCS hit lists. Interestingly, shape-based ranking of MGBs versus FDA-approved drugs again leads to high enrichment rates, indicating complementary coverage of chemical shape space and indicating minor groove affinity to be unfavorable for approval of drugs targeting proteins.
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Affiliation(s)
- Julian E Fuchs
- Faculty of Chemistry and Pharmacy, University of Innsbruck, Innsbruck, Austria
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