1
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Iijima D, Sugama H, Awai N, Takahashi Y, Togashi Y, Takebe T, Xie J, Shen J, Ke Y, Akatsuka H, Kawaguchi T, Takedomi K, Kashima A, Nishio M, Inui Y, Yoneda H, Xia G, Iijima T. Discovery of Novel 2-Carbamoyl Morpholine Derivatives as Highly Potent and Orally Active Direct Renin Inhibitors. ACS Med Chem Lett 2022; 13:1351-1357. [PMID: 35978678 PMCID: PMC9377009 DOI: 10.1021/acsmedchemlett.2c00280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/26/2022] [Indexed: 12/31/2022] Open
Abstract
The renin-angiotensin-aldosterone system (RAAS) plays a key role in the regulation of blood pressure. Renin, the first and rate-limiting enzyme of the RAAS, is an attractive target for the treatment of hypertension and cardiovascular/renal diseases. Therefore, various direct renin inhibitors (DRIs) have been researched over recent decades; however, most exhibited poor pharmacokinetics and oral bioavailability due to the peptidomimetic or nonpeptidomimetic structures with a molecular weight (MW) of >600, and only aliskiren is approved. This study introduces a novel class of DRIs comprised of a 2-carbamoyl morpholine scaffold. These compounds have a nonpeptidomimetic structure and a MW of <500. The representative compound 26 was highly potent despite not occupying S1'-S2' sites or the opened flap region used by other DRIs and exerted a significant antihypertensive efficacy via oral administration on double transgenic mice carrying both the human angiotensinogen and the human renin genes.
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Affiliation(s)
- Daisuke Iijima
- Sohyaku,
Innovative Research Division, Mitsubishi
Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Hiroshi Sugama
- Sohyaku,
Innovative Research Division, Mitsubishi
Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Nobumasa Awai
- Sohyaku,
Innovative Research Division, Mitsubishi
Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Yoichi Takahashi
- Sohyaku,
Innovative Research Division, Mitsubishi
Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Yuko Togashi
- Sohyaku,
Innovative Research Division, Mitsubishi
Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Tohru Takebe
- Sohyaku,
Innovative Research Division, Mitsubishi
Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Jianshu Xie
- Central
Research Institute, Shanghai Pharmaceuticals
Holding Co., Ltd., Building 5, No. 898 Halei Road, Zhangjiang Hi-tech Park, Pudong New
Area, Shanghai 201203, PR China
| | - Jingkang Shen
- Central
Research Institute, Shanghai Pharmaceuticals
Holding Co., Ltd., Building 5, No. 898 Halei Road, Zhangjiang Hi-tech Park, Pudong New
Area, Shanghai 201203, PR China
| | - Ying Ke
- Central
Research Institute, Shanghai Pharmaceuticals
Holding Co., Ltd., Building 5, No. 898 Halei Road, Zhangjiang Hi-tech Park, Pudong New
Area, Shanghai 201203, PR China
| | - Hidenori Akatsuka
- Sohyaku,
Innovative Research Division, Mitsubishi
Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Takayuki Kawaguchi
- Sohyaku,
Innovative Research Division, Mitsubishi
Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Kei Takedomi
- Sohyaku,
Innovative Research Division, Mitsubishi
Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Akiko Kashima
- Sohyaku,
Innovative Research Division, Mitsubishi
Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Masashi Nishio
- Sohyaku,
Innovative Research Division, Mitsubishi
Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Yosuke Inui
- Sohyaku,
Innovative Research Division, Mitsubishi
Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Hikaru Yoneda
- Sohyaku,
Innovative Research Division, Mitsubishi
Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Guangxin Xia
- Central
Research Institute, Shanghai Pharmaceuticals
Holding Co., Ltd., Building 5, No. 898 Halei Road, Zhangjiang Hi-tech Park, Pudong New
Area, Shanghai 201203, PR China
| | - Toru Iijima
- Sohyaku,
Innovative Research Division, Mitsubishi
Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
- Lead
Exploration Unit, Drug Discovery Initiative, Graduate School of Pharmaceutical
Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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2
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Iijima D, Sugama H, Takahashi Y, Hirai M, Togashi Y, Xie J, Shen J, Ke Y, Akatsuka H, Kawaguchi T, Takedomi K, Kashima A, Nishio M, Inui Y, Yoneda H, Xia G, Iijima T. Discovery of SPH3127: A Novel, Highly Potent, and Orally Active Direct Renin Inhibitor. J Med Chem 2022; 65:10882-10897. [PMID: 35939295 DOI: 10.1021/acs.jmedchem.2c00834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Renin is the rate-limiting enzyme in the renin-angiotensin-aldosterone system (RAAS) which regulates blood pressure and renal function and hence is an attractive target for the treatment of hypertension and cardiovascular/renal diseases. However, the development of direct renin inhibitors (DRIs) with favorable oral bioavailability has been a longstanding challenge for many years. This problem was thought to be because most of the reported DRIs were peptide-like structures or nonpeptide-like structures with a molecular weight (MW) of > 600. Therefore, we tried to find nonpeptidomimetic DRIs with a MW of < 500 and discovered the promising 2-carbamoyl morpholine derivative 4. In our efforts to improve the pharmacokinetic profile of 4 without a significant increase in the MW, we discovered compound 18 (SPH3127), which demonstrated higher bioavailability and a more potent antihypertensive effect in preclinical models than aliskiren and has completed a phase II clinical trial for essential hypertension.
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Affiliation(s)
- Daisuke Iijima
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Hiroshi Sugama
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Yoichi Takahashi
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Miki Hirai
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Yuko Togashi
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Jianshu Xie
- Central Research Institute, Shanghai Pharmaceuticals Holding Co., Ltd., Building 5, No. 898 Halei Road, Zhangjiang Hi-tech Park, Pudong New Area, Shanghai 201203, PR China
| | - Jingkang Shen
- Central Research Institute, Shanghai Pharmaceuticals Holding Co., Ltd., Building 5, No. 898 Halei Road, Zhangjiang Hi-tech Park, Pudong New Area, Shanghai 201203, PR China
| | - Ying Ke
- Central Research Institute, Shanghai Pharmaceuticals Holding Co., Ltd., Building 5, No. 898 Halei Road, Zhangjiang Hi-tech Park, Pudong New Area, Shanghai 201203, PR China
| | - Hidenori Akatsuka
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Takayuki Kawaguchi
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Kei Takedomi
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Akiko Kashima
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Masashi Nishio
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Yosuke Inui
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Hikaru Yoneda
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan
| | - Guangxin Xia
- Central Research Institute, Shanghai Pharmaceuticals Holding Co., Ltd., Building 5, No. 898 Halei Road, Zhangjiang Hi-tech Park, Pudong New Area, Shanghai 201203, PR China
| | - Toru Iijima
- Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan.,Lead Exploration Unit, Drug Discovery Initiative, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Kuhn B, Haap W, Obst-Sander U, Kramer C, Stahl M. What We Learned in 25 Years of Interactive Molecular Design Sessions. ChemMedChem 2021; 16:2760-2763. [PMID: 34374230 DOI: 10.1002/cmdc.202100351] [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: 05/20/2021] [Indexed: 11/12/2022]
Abstract
We retrace Prof. François Diederich's consultancy work for Roche and its impact over the years he worked with us. François Diederich uniquely shaped our approach to molecular design, and interactions with him and his research group at ETH Zurich have created deep insights into molecular recognition. Herein we share how his style and approach continue to inspire us.
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Affiliation(s)
- Bernd Kuhn
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070, Basel, Switzerland
| | - Wolfgang Haap
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070, Basel, Switzerland
| | - Ulrike Obst-Sander
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070, Basel, Switzerland
| | - Christian Kramer
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070, Basel, Switzerland
| | - Martin Stahl
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070, Basel, Switzerland
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4
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Bhakat S. Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation with biophysical experiments. RSC Adv 2021; 11:11026-11047. [PMID: 35423571 PMCID: PMC8695779 DOI: 10.1039/d0ra10359d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/21/2021] [Indexed: 01/26/2023] Open
Abstract
Pepsin-like aspartic proteases (PAPs) are a class of aspartic proteases which shares tremendous structural similarity with human pepsin. One of the key structural features of PAPs is the presence of a β-hairpin motif otherwise known as flap. The biological function of the PAPs is highly dependent on the conformational dynamics of the flap region. In apo PAPs, the conformational dynamics of the flap is dominated by the rotational degrees of freedom associated with χ1 and χ2 angles of conserved Tyr (or Phe in some cases). However it is plausible that dihedral order parameters associated with several other residues might play crucial roles in the conformational dynamics of apo PAPs. Due to their size, complexities associated with conformational dynamics and clinical significance (drug targets for malaria, Alzheimer's disease etc.), PAPs provide a challenging testing ground for computational and experimental methods focusing on understanding conformational dynamics and molecular recognition in biomolecules. The opening of the flap region is necessary to accommodate substrate/ligand in the active site of the PAPs. The BIG challenge is to gain atomistic details into how reversible ligand binding/unbinding (molecular recognition) affects the conformational dynamics. Recent reports of kinetics (K i, K d) and thermodynamic parameters (ΔH, TΔS, and ΔG) associated with macro-cyclic ligands bound to BACE1 (belongs to PAP family) provide a perfect challenge (how to deal with big ligands with multiple torsional angles and select optimum order parameters to study reversible ligand binding/unbinding) for computational methods to predict binding free energies and kinetics beyond typical test systems e.g. benzamide-trypsin. In this work, i reviewed several order parameters which were proposed to capture the conformational dynamics and molecular recognition in PAPs. I further highlighted how machine learning methods can be used as order parameters in the context of PAPs. I then proposed some open ideas and challenges in the context of molecular simulation and put forward my case on how biophysical experiments e.g. NMR, time-resolved FRET etc. can be used in conjunction with biomolecular simulation to gain complete atomistic insights into the conformational dynamics of PAPs.
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Affiliation(s)
- Soumendranath Bhakat
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University P. O. Box 124 SE-22100 Lund Sweden +46-769608418
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5
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Short enantioselective total synthesis of (+)-tofacitinib. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.152838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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6
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Ramya K, Suresh R, Kumar HY, Kumar BRP, Murthy NBS. Decades-old renin inhibitors are still struggling to find a niche in antihypertensive therapy. A fleeting look at the old and the promising new molecules. Bioorg Med Chem 2020; 28:115466. [PMID: 32247750 PMCID: PMC7112834 DOI: 10.1016/j.bmc.2020.115466] [Citation(s) in RCA: 9] [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: 01/17/2020] [Revised: 03/24/2020] [Accepted: 03/24/2020] [Indexed: 12/20/2022]
Abstract
Hypertension is a diverse illness interlinked with cerebral, cardiovascular (CVS) and renal abnormalities. Presently, the malady is being treated by focusing on Renin- angiotensin system (RAS), voltage-gated calcium channels, peripheral vasodilators, renal and sympathetic nervous systems. Cardiovascular and renal abnormalities are associated with the overactivation of RAS, which can be constrained by angiotensin- converting enzyme inhibitors (ACEIs), angiotensin II (Ang-II) -AT1 receptor blockers (ARBs) and renin inhibitors. The latter is a new player in the old system. The renin catalyzes the conversion of angiotensinogen to Angiotensin I (Ang-I). This can be overcome by inhibiting renin, a preliminary step, eventually hinders the occurrence of the cascade of events in the RAS. Various peptidomimetics, the first-generation renin inhibitors developed six decades ago have limited drug-like properties as they suffered from poor intestinal absorption, high liver first-pass metabolism and low oral bioavailability. The development of chemically diverse molecules from peptides to nonpeptides expanded the horizon to achieving direct renin inhibition. Aliskiren, a blockbuster drug that emerged as a clinical candidate and got approved by the US FDA in 2007 was developed by molecular modeling studies. Aliskiren indicated superior to average efficacy and with minor adverse effects relative to other RAS inhibitors. However, its therapeutic use is limited by poor oral bioavailability of less than 2% that is similar to first-generation peptidic compounds. In this review, we present the development of direct renin inhibitors (DRIs) from peptidic to nonpeptidics that lead to the birth of aliskiren, its place in the treatment of cardiovascular diseases and its limitations.
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Affiliation(s)
- Krishnappa Ramya
- Department of Pharmaceutical Chemistry, Oxbridge College of Pharmacy, Mahadeshwara Nagara, Bengaluru 560091, Karnataka, India; Department of Pharmacy, Annamalai University, Annamalai nagar, Chidambaram 608002, Tamilnadu, India.
| | - Ramalingam Suresh
- Department of Pharmacy, Annamalai University, Annamalai nagar, Chidambaram 608002, Tamilnadu, India
| | - Honnavalli Yogish Kumar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research (JSS AHER), SS Nagara, Mysuru 570015, Karnataka, India
| | - B R Prashantha Kumar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research (JSS AHER), SS Nagara, Mysuru 570015, Karnataka, India
| | - N B Sridhara Murthy
- Department of Pharmaceutical Chemistry, Oxbridge College of Pharmacy, Mahadeshwara Nagara, Bengaluru 560091, Karnataka, India
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7
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Cheuka PM, Dziwornu G, Okombo J, Chibale K. Plasmepsin Inhibitors in Antimalarial Drug Discovery: Medicinal Chemistry and Target Validation (2000 to Present). J Med Chem 2020; 63:4445-4467. [PMID: 31913032 DOI: 10.1021/acs.jmedchem.9b01622] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Plasmepsins represent novel antimalarial drug targets. However, plasmepsin-based antimalarial drug discovery efforts in the past 2 decades have generally suffered some drawbacks including lack of translatability of target inhibition to potent parasite inhibition in vitro and in vivo as well as poor selectivity over the related human aspartic proteases. Most studies reported in this period have over-relied on the use of hemoglobinase plasmepsins I-IV (particularly I and II) as targets for the new inhibitors even though these are known to be nonessential at the asexual stage of parasite development. Therefore, future antimalarial drug discovery efforts seeking to identify plasmepsin inhibitors should focus on incorporating non-hemoglobinase plasmepsins such as V, IX, and X in their screening in order to maximize chances of success. Additionally, there is need to go beyond just target enzymatic activity profiling to establishing cellular activity, physicochemical as well as drug metabolism and pharmacokinetics properties and finally in vivo proof-of-concept while ensuring selectivity over related human host proteases.
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Affiliation(s)
- Peter Mubanga Cheuka
- Department of Chemistry, University of Zambia, Great East Road Campus, P.O. Box 32379, Lusaka, Zambia
| | - Godwin Dziwornu
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - John Okombo
- Department of Microbiology and Immunology, Columbia University, 701 West 168th Street, New York, New York 10032, United States
| | - Kelly Chibale
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.,Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa.,South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
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8
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Bobrovs R, Jaudzems K, Jirgensons A. Exploiting Structural Dynamics To Design Open-Flap Inhibitors of Malarial Aspartic Proteases. J Med Chem 2019; 62:8931-8950. [DOI: 10.1021/acs.jmedchem.9b00184] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Raitis Bobrovs
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV1006, Latvia
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9
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Ben Bdira F, Jiang J, Kallemeijn W, de Haan A, Florea BI, Bleijlevens B, Boot R, Overkleeft HS, Aerts JM, Ubbink M. Hydrophobic Interactions Contribute to Conformational Stabilization of Endoglycoceramidase II by Mechanism-Based Probes. Biochemistry 2016; 55:4823-35. [DOI: 10.1021/acs.biochem.6b00363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fredj Ben Bdira
- Department
of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Jianbing Jiang
- Department
of Bio-organic Synthesis, Leiden Institute of Chemistry, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Wouter Kallemeijn
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Annett de Haan
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Bogdan I. Florea
- Department
of Bio-organic Synthesis, Leiden Institute of Chemistry, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Boris Bleijlevens
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Rolf Boot
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Herman S. Overkleeft
- Department
of Bio-organic Synthesis, Leiden Institute of Chemistry, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Johannes M. Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Marcellus Ubbink
- Department
of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg
55, 2333 CC Leiden, The Netherlands
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10
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Kuhn B, Guba W, Hert J, Banner D, Bissantz C, Ceccarelli S, Haap W, Körner M, Kuglstatter A, Lerner C, Mattei P, Neidhart W, Pinard E, Rudolph MG, Schulz-Gasch T, Woltering T, Stahl M. A Real-World Perspective on Molecular Design. J Med Chem 2016; 59:4087-102. [PMID: 26878596 DOI: 10.1021/acs.jmedchem.5b01875] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects, with the aim of highlighting those methods that provide real added value. Our brief accounts encompass a broad range of methods and techniques applied to a variety of enzymes and receptors. Most of these are based on judicious application of knowledge about molecular conformations and interactions: filling of lipophilic pockets to gain affinity or selectivity, addition of polar substituents, scaffold hopping, transfer of SAR, conformation analysis, and molecular overlays. A case study of sequence-driven focused screening is presented to illustrate how appropriate preprocessing of information enables effective exploitation of prior knowledge. We conclude that qualitative statements enabling chemists to focus on promising regions of chemical space are often more impactful than quantitative prediction.
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Affiliation(s)
- Bernd Kuhn
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Wolfgang Guba
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Jérôme Hert
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - David Banner
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Caterina Bissantz
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Simona Ceccarelli
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Wolfgang Haap
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Matthias Körner
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Andreas Kuglstatter
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Christian Lerner
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Patrizio Mattei
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Werner Neidhart
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Emmanuel Pinard
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Markus G Rudolph
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Tanja Schulz-Gasch
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Thomas Woltering
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Martin Stahl
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland
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11
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Huang WX, Wu B, Gao X, Chen MW, Wang B, Zhou YG. Iridium-Catalyzed Selective Hydrogenation of 3-Hydroxypyridinium Salts: A Facile Synthesis of Piperidin-3-ones. Org Lett 2015; 17:1640-3. [DOI: 10.1021/acs.orglett.5b00276] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Wen-Xue Huang
- State Key Laboratory of Fine Chemicals, School of Pharmaceutical
Science and Technology, Dalian University of Technology, 2 Linggong
Road, Dalian 116024, P. R. China
- State Key Laboratory of Catalysis, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan
Road, Dalian 116023, P. R. China
| | - Bo Wu
- State Key Laboratory of Catalysis, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan
Road, Dalian 116023, P. R. China
| | - Xiang Gao
- State Key Laboratory of Catalysis, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan
Road, Dalian 116023, P. R. China
| | - Mu-Wang Chen
- State Key Laboratory of Catalysis, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan
Road, Dalian 116023, P. R. China
| | - Baomin Wang
- State Key Laboratory of Fine Chemicals, School of Pharmaceutical
Science and Technology, Dalian University of Technology, 2 Linggong
Road, Dalian 116024, P. R. China
| | - Yong-Gui Zhou
- State Key Laboratory of Catalysis, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan
Road, Dalian 116023, P. R. China
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12
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Huizing AP, Mondal M, Hirsch AKH. Fighting malaria: structure-guided discovery of nonpeptidomimetic plasmepsin inhibitors. J Med Chem 2015; 58:5151-63. [PMID: 25719272 DOI: 10.1021/jm5014133] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plasmepsins (Plms) are aspartic proteases involved in the degradation of human hemoglobin by Plasmodium falciparum. Given that the parasite needs the resulting amino acid building blocks for its growth and development, plasmepsins are an important antimalarial drug target. Over the past decade, tremendous progress has been achieved in the development of inhibitors of plasmepsin using two strategies: structure-based drug design (SBDD) and structure-based virtual screening (SBVS). Herein, we review the inhibitors of Plms I-IV developed by SBDD or SBVS with a particular focus on obtaining selectivity versus the human Asp proteases cathepsins and renin and activity in cell-based assays. By use of SBDD, the flap pocket of Plm II has been discovered and constitutes a convenient handle to obtain selectivity. In SBVS, activity against Plms I-IV and selectivity versus cathepsins are not always taken into account. A combination of SBVS, SBDD, and molecular dynamics simulations opens up opportunities for future design cycles.
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Affiliation(s)
- Anja P Huizing
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747 AG Groningen, The Netherlands
| | - Milon Mondal
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747 AG Groningen, The Netherlands
| | - Anna K H Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747 AG Groningen, The Netherlands
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13
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Murakami K, Sasano Y, Tomizawa M, Shibuya M, Kwon E, Iwabuchi Y. Highly Enantioselective Organocatalytic Oxidative Kinetic Resolution of Secondary Alcohols Using Chiral Alkoxyamines as Precatalysts: Catalyst Structure, Active Species, and Substrate Scope. J Am Chem Soc 2014; 136:17591-600. [DOI: 10.1021/ja509766f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Keiichi Murakami
- Department of Organic Chemistry,
Graduate School of Pharmaceutical
Sciences and ‡Research and Analytical Center for Giant Molecules, Graduate School
of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Yusuke Sasano
- Department of Organic Chemistry,
Graduate School of Pharmaceutical
Sciences and ‡Research and Analytical Center for Giant Molecules, Graduate School
of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Masaki Tomizawa
- Department of Organic Chemistry,
Graduate School of Pharmaceutical
Sciences and ‡Research and Analytical Center for Giant Molecules, Graduate School
of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Masatoshi Shibuya
- Department of Organic Chemistry,
Graduate School of Pharmaceutical
Sciences and ‡Research and Analytical Center for Giant Molecules, Graduate School
of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Eunsang Kwon
- Department of Organic Chemistry,
Graduate School of Pharmaceutical
Sciences and ‡Research and Analytical Center for Giant Molecules, Graduate School
of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Yoshiharu Iwabuchi
- Department of Organic Chemistry,
Graduate School of Pharmaceutical
Sciences and ‡Research and Analytical Center for Giant Molecules, Graduate School
of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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14
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Mateo-Marti E, Pradier CM. UV irradiation study of a tripeptide isolated in an argon matrix: a tautomerism process evidenced by infrared and X-ray photoemission spectroscopies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 109:247-252. [PMID: 23542515 DOI: 10.1016/j.saa.2013.02.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 02/14/2013] [Accepted: 02/16/2013] [Indexed: 06/02/2023]
Abstract
Matrix isolation is a powerful tool for studying photochemical processes occurring in isolated molecules. In this way, we characterized the chemical modifications occurring within a tri peptide molecule, IGF, when exposed to the influence of Ultraviolet (UV) irradiation. This paper first describes the successful formation of the tripeptide (IGF) argon matrix under vacuum conditions, followed by the in situ UV irradiation and characterization of the molecular matrix reactivity after UV-irradiation. These studies have been performed by combining two complementary spectroscopic techniques, Fourier-Transform Reflexion Absorption Spectroscopy (FT-IRRAS) and X-ray Photoelectron Spectroscopy (XPS). The IR spectra of the isolated peptide-matrix, before and after UV irradiation, revealed significant differences that could be associated either to a partial deprotonation of the molecule or to a tautomeric conversion of some amide bonds to imide ones on some peptide molecules. XPS analyses undoubtedly confirmed the second hypothesis; the combination of IRRAS and XPS results provide evidence that UV irradiation of peptides induces a chemical reaction, namely a shift of the double bond, meaning partial conversion from amide tautomer into an imidic acid tautomer.
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Affiliation(s)
- E Mateo-Marti
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain.
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15
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Stamford A, Strickland C. Inhibitors of BACE for treating Alzheimer's disease: a fragment-based drug discovery story. Curr Opin Chem Biol 2013; 17:320-8. [PMID: 23683349 DOI: 10.1016/j.cbpa.2013.04.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 04/02/2013] [Accepted: 04/15/2013] [Indexed: 11/27/2022]
Abstract
Several fragment-based methods have been applied to the discovery of new lead sources for inhibitors of BACE1, an important therapeutic target for Alzheimer's disease. Among the most common fragment hits were various amidine-containing molecules in which the amidine engaged in discrete H-bond donor-acceptor interaction with the BACE1 catalytic dyad. Structure and medicinal chemistry knowledge-based optimization with emphasis on ligand efficiency resulted in identification of a key pharmacophore comprising a non-planar cyclic amidine scaffold directly attached to a phenyl group projecting into S1. This key pharmacophore is a common feature of known clinical candidates and has dominated the recent patent literature. A structural comparison of the non-planar cyclic amidine motif with other BACE1 pharmacophores highlights its uniqueness and distinct advantages.
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Affiliation(s)
- Andrew Stamford
- Merck Research Laboratories, 126 East Lincoln Avenue, Rahway, NJ 07065, United States.
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16
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Yokokawa F. Recent progress on the discovery of non-peptidic direct renin inhibitors for the clinical management of hypertension. Expert Opin Drug Discov 2013; 8:673-90. [DOI: 10.1517/17460441.2013.791279] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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17
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Yuan J, Venkatraman S, Zheng Y, McKeever BM, Dillard LW, Singh SB. Structure-based design of β-site APP cleaving enzyme 1 (BACE1) inhibitors for the treatment of Alzheimer's disease. J Med Chem 2013; 56:4156-80. [PMID: 23509904 DOI: 10.1021/jm301659n] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The amyloid hypothesis asserts that excess production or reduced clearance of the amyloid-β (Aβ) peptides in the brain initiates a sequence of events that ultimately lead to Alzheimer's disease and dementia. The Aβ hypothesis has identified BACE1 as a therapeutic target to treat Alzheimer's and led to medicinal chemistry efforts to design its inhibitors both in the pharmaceutical industry and in academia. This review summarizes two distinct categories of inhibitors designed based on conformational states of "closed" and "open" forms of the enzyme. In each category the inhibitors are classified based on the core catalytic interaction group or the aspartyl binding motif (ABM). This review covers the description of inhibitors in each ABM class with X-ray crystal structures of key compounds, their binding modes, related structure-activity data highlighting potency advances, and additional properties such as selectivity profile, P-gp efflux, pharmacokinetic, and pharmacodynamic data.
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Affiliation(s)
- Jing Yuan
- Vitae Pharmaceuticals, 502 W. Office Center Drive, Fort Washington, Pennsylvania 19034, USA
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18
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Song Y, Jin H, Liu X, Zhu L, Huang J, Li H. Discovery of non-peptide inhibitors of Plasmepsin II by structure-based virtual screening. Bioorg Med Chem Lett 2013; 23:2078-82. [DOI: 10.1016/j.bmcl.2013.01.128] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 01/26/2013] [Accepted: 01/30/2013] [Indexed: 10/27/2022]
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19
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Lorthiois E, Breitenstein W, Cumin F, Ehrhardt C, Francotte E, Jacoby E, Ostermann N, Sellner H, Kosaka T, Webb RL, Rigel DF, Hassiepen U, Richert P, Wagner T, Maibaum J. The discovery of novel potent trans-3,4-disubstituted pyrrolidine inhibitors of the human aspartic protease renin from in silico three-dimensional (3D) pharmacophore searches. J Med Chem 2013; 56:2207-17. [PMID: 23425156 DOI: 10.1021/jm3017078] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The small-molecule trans-3,4-disubstituted pyrrolidine 6 was identified from in silico three-dimensional (3D) pharmacophore searches based on known X-ray structures of renin-inhibitor complexes and demonstrated to be a weakly active inhibitor of the human enzyme. The unexpected binding mode of the more potent enantiomer (3S,4S)-6a in an extended conformation spanning the nonprime and S1' pockets of the recombinant human (rh)-renin active site was elucidated by X-ray crystallography. Initial structure-activity relationship work focused on modifications of the hydrophobic diphenylamine portion positioned in S1 and extending toward the S2 pocket. Replacement with an optimized P3-P1 pharmacophore interacting to the nonsubstrate S3(sp) cavity eventually resulted in significantly improved in vitro potency and selectivity. The prototype analogue (3S,4S)-12a of this new class of direct renin inhibitors exerted blood pressure lowering effects in a hypertensive double-transgenic rat model after oral administration.
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Affiliation(s)
- Edwige Lorthiois
- Novartis Pharma AG, Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland.
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20
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Lee CW, Lira R, Dutra J, Ogilvie K, O’Neill BT, Brodney M, Helal C, Young J, Lachapelle E, Sakya S, Murray JC. Stereoselective Synthesis of Spiropiperidines as BACE-1 Aspartyl Protease Inhibitors via Late Stage N-Arylation of a 1,8-Diazaspiro[4.5]dec-3-en-2-one Pharmacophore. J Org Chem 2013; 78:2661-9. [DOI: 10.1021/jo400016m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Che-Wah Lee
- Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry, Eastern
Point Road, Groton, Connecticut
06340, United States
| | - Ricardo Lira
- Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry, Eastern
Point Road, Groton, Connecticut
06340, United States
| | - Jason Dutra
- Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry, Eastern
Point Road, Groton, Connecticut
06340, United States
| | - Kevin Ogilvie
- Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry, Eastern
Point Road, Groton, Connecticut
06340, United States
| | - Brian T. O’Neill
- Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry, Eastern
Point Road, Groton, Connecticut
06340, United States
| | - Michael Brodney
- Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry, Eastern
Point Road, Groton, Connecticut
06340, United States
| | - Christopher Helal
- Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry, Eastern
Point Road, Groton, Connecticut
06340, United States
| | - Joseph Young
- Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry, Eastern
Point Road, Groton, Connecticut
06340, United States
| | - Erik Lachapelle
- Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry, Eastern
Point Road, Groton, Connecticut
06340, United States
| | - Subas Sakya
- Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry, Eastern
Point Road, Groton, Connecticut
06340, United States
| | - John C. Murray
- Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry, Eastern
Point Road, Groton, Connecticut
06340, United States
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21
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Synthesis of 2-aminomethyl-4-phenyl-1-azabicyclo[2.2.1]heptanes via LiAlH4-induced reductive cyclization of 2-(4-chloro-2-cyano-2-phenylbutyl)aziridines and evaluation of their antimalarial activity. Bioorg Med Chem Lett 2013; 23:1507-10. [DOI: 10.1016/j.bmcl.2012.12.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 12/07/2012] [Accepted: 12/10/2012] [Indexed: 11/22/2022]
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22
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Harmsen RAG, Sivertsen A, Michetti D, Brandsdal BO, Sydnes LK, Haug BE. Synthesis and docking of novel piperidine renin inhibitors. MONATSHEFTE FUR CHEMIE 2013. [DOI: 10.1007/s00706-012-0903-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Mori Y, Ogawa Y, Mochizuki A, Nakamura Y, Sugita C, Miyazaki S, Tamaki K, Matsui Y, Takahashi M, Nagayama T, Nagai Y, Inoue SI, Nishi T. Design and discovery of new (3S,5R)-5-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]piperidine-3-carboxamides as potent renin inhibitors. Bioorg Med Chem Lett 2012; 22:7677-82. [PMID: 23122821 DOI: 10.1016/j.bmcl.2012.09.103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 09/25/2012] [Accepted: 09/28/2012] [Indexed: 11/16/2022]
Abstract
Utilizing X-ray crystal structure analysis, (3S,5R)-5-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]piperidine-3-carboxamides were designed and identified as renin inhibitors. The most potent compound 15 demonstrated favorable pharmacokinetic and pharmacodynamic profiles in rat.
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Affiliation(s)
- Yutaka Mori
- Lead Discovery & Optimization Research Laboratories I, Daiichi Sankyo Co., Ltd, 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
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24
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Affiliation(s)
- Alexander Dömling
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA.
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25
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Bhaumik P, Gustchina A, Wlodawer A. Structural studies of vacuolar plasmepsins. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1824:207-23. [PMID: 21540129 PMCID: PMC3154504 DOI: 10.1016/j.bbapap.2011.04.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2011] [Revised: 04/11/2011] [Accepted: 04/12/2011] [Indexed: 10/18/2022]
Abstract
Plasmepsins (PMs) are pepsin-like aspartic proteases present in different species of parasite Plasmodium. Four Plasmodium spp. (P. vivax, P. ovale, P. malariae, and the most lethal P. falciparum) are mainly responsible for causing human malaria that affects millions worldwide. Due to the complexity and rate of parasite mutation coupled with regional variations, and the emergence of P. falciparum strains which are resistant to antimalarial agents such as chloroquine and sulfadoxine/pyrimethamine, there is constant pressure to find new and lasting chemotherapeutic drug therapies. Since many proteases represent therapeutic targets and PMs have been shown to play an important role in the survival of parasite, these enzymes have recently been identified as promising targets for the development of novel antimalarial drugs. The genome of P. falciparum encodes 10 PMs (PMI, PMII, PMIV-X and histo-aspartic protease (HAP)), 4 of which (PMI, PMII, PMIV and HAP) reside within the food vacuole, are directly involved in degradation of human hemoglobin, and share 50-79% amino acid sequence identity. This review focuses on structural studies of only these four enzymes, including their orthologs in other Plasmodium spp.. Almost all original crystallographic studies were performed with PMII, but more recent work on PMIV, PMI, and HAP resulted in a more complete picture of the structure-function relationship of vacuolar PMs. Many structures of inhibitor complexes of vacuolar plasmepsins, as well as their zymogens, have been reported in the last 15 years. Information gained by such studies will be helpful for the development of better inhibitors that could become a new class of potent antimalarial drugs. This article is part of a Special Issue entitled: Proteolysis 50 years after the discovery of lysosome.
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Affiliation(s)
- Prasenjit Bhaumik
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Alla Gustchina
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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26
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Loughlin WA, Tyndall JDA, Glenn MP, Hill TA, Fairlie DP. Update 1 of: Beta-Strand Mimetics. Chem Rev 2011; 110:PR32-69. [DOI: 10.1021/cr900395y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wendy A. Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Joel D. A. Tyndall
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Matthew P. Glenn
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Timothy A. Hill
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - David P. Fairlie
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
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27
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Cole DC, Bursavich MG. Nonpeptide BACE1 Inhibitors: Design and Synthesis. ASPARTIC ACID PROTEASES AS THERAPEUTIC TARGETS 2011. [DOI: 10.1002/9783527630943.ch17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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28
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29
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Aspiotis R, Chen A, Cauchon E, Dubé D, Falgueyret JP, Gagné S, Gallant M, Grimm EL, Houle R, Juteau H, Lacombe P, Laliberté S, Lévesque JF, MacDonald D, McKay D, Percival MD, Roy P, Soisson SM, Wu T. The discovery and synthesis of potent zwitterionic inhibitors of renin. Bioorg Med Chem Lett 2011; 21:2430-6. [DOI: 10.1016/j.bmcl.2011.02.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 02/15/2011] [Indexed: 11/26/2022]
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30
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Recent trends and observations in the design of high-quality screening collections. Future Med Chem 2011; 3:751-66. [DOI: 10.4155/fmc.11.15] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The design of a high-quality screening collection is of utmost importance for the early drug-discovery process and provides, in combination with high-quality assay systems, the foundation of future discoveries. Herein, we review recent trends and observations to successfully expand the access to bioactive chemical space, including the feedback from hit assessment interviews of high-throughput screening campaigns; recent successes with chemogenomics target family approaches, the identification of new relevant target/domain families, diversity-oriented synthesis and new emerging compound classes, and non-classical approaches, such as fragment-based screening and DNA-encoded chemical libraries. The role of in silico library design approaches are emphasized.
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31
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Design and optimization of new piperidines as renin inhibitors. Bioorg Med Chem Lett 2010; 20:6286-90. [DOI: 10.1016/j.bmcl.2010.08.086] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 08/17/2010] [Accepted: 08/17/2010] [Indexed: 11/22/2022]
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32
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Webb RL, Schiering N, Sedrani R, Maibaum J. Direct Renin Inhibitors as a New Therapy for Hypertension. J Med Chem 2010; 53:7490-520. [DOI: 10.1021/jm901885s] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Randy L. Webb
- Novartis Pharmaceuticals Corp., Institutes for BioMedical Research, East Hanover, New Jersey
| | - Nikolaus Schiering
- Novartis Pharma AG, Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Richard Sedrani
- Novartis Pharma AG, Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Jürgen Maibaum
- Novartis Pharma AG, Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
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33
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Bower JF, Rujirawanich J, Gallagher T. N-Heterocycle construction via cyclic sulfamidates. Applications in synthesis. Org Biomol Chem 2010; 8:1505-19. [DOI: 10.1039/b921842d] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Remeň L, Bezençon O, Richard-Bildstein S, Bur D, Prade L, Corminboeuf O, Boss C, Grisostomi C, Sifferlen T, Strickner P, Hess P, Delahaye S, Treiber A, Weller T, Binkert C, Steiner B, Fischli W. New classes of potent and bioavailable human renin inhibitors. Bioorg Med Chem Lett 2009; 19:6762-5. [PMID: 19853442 DOI: 10.1016/j.bmcl.2009.09.104] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Revised: 09/24/2009] [Accepted: 09/24/2009] [Indexed: 10/20/2022]
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35
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Bezençon O, Bur D, Weller T, Richard-Bildstein S, Remeň L, Sifferlen T, Corminboeuf O, Grisostomi C, Boss C, Prade L, Delahaye S, Treiber A, Strickner P, Binkert C, Hess P, Steiner B, Fischli W. Design and Preparation of Potent, Nonpeptidic, Bioavailable Renin Inhibitors. J Med Chem 2009; 52:3689-702. [DOI: 10.1021/jm900022f] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Olivier Bezençon
- Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Daniel Bur
- Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Thomas Weller
- Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Sylvia Richard-Bildstein
- Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Luboš Remeň
- Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Thierry Sifferlen
- Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Olivier Corminboeuf
- Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Corinna Grisostomi
- Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Christoph Boss
- Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Lars Prade
- Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Stéphane Delahaye
- Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Alexander Treiber
- Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Panja Strickner
- Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Christoph Binkert
- Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Patrick Hess
- Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Beat Steiner
- Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Walter Fischli
- Drug Discovery and Preclinical Research, Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
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36
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Bhaumik P, Xiao H, Parr CL, Kiso Y, Gustchina A, Yada RY, Wlodawer A. Crystal structures of the histo-aspartic protease (HAP) from Plasmodium falciparum. J Mol Biol 2009; 388:520-40. [PMID: 19285084 DOI: 10.1016/j.jmb.2009.03.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Revised: 02/25/2009] [Accepted: 03/05/2009] [Indexed: 02/07/2023]
Abstract
The structures of recombinant histo-aspartic protease (HAP) from malaria-causing parasite Plasmodium falciparum as apoenzyme and in complex with two inhibitors, pepstatin A and KNI-10006, were solved at 2.5-, 3.3-, and 3.05-A resolutions, respectively. In the apoenzyme crystals, HAP forms a tight dimer not seen previously in any aspartic protease. The interactions between the monomers affect the conformation of two flexible loops, the functionally important "flap" (residues 70-83) and its structural equivalent in the C-terminal domain (residues 238-245), as well as the orientation of helix 225-235. The flap is found in an open conformation in the apoenzyme. Unexpectedly, the active site of the apoenzyme contains a zinc ion tightly bound to His32 and Asp215 from one monomer and to Glu278A from the other monomer, with the coordination of Zn resembling that seen in metalloproteases. The flap is closed in the structure of the pepstatin A complex, whereas it is open in the complex with KNI-10006. Although the binding mode of pepstatin A is significantly different from that in other pepsin-like aspartic proteases, its location in the active site makes unlikely the previously proposed hypothesis that HAP is a serine protease. The binding mode of KNI-10006 is unusual compared with the binding of other inhibitors from the KNI series to aspartic proteases. The novel features of the HAP active site could facilitate design of specific inhibitors used in the development of antimalarial drugs.
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Affiliation(s)
- Prasenjit Bhaumik
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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Luksch T, Chan NS, Brass S, Sotriffer C, Klebe G, Diederich W. Computer-Aided Design and Synthesis of Nonpeptidic Plasmepsin II and IV Inhibitors. ChemMedChem 2008; 3:1323-36. [DOI: 10.1002/cmdc.200700270] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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38
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Blum A, Böttcher J, Sammet B, Luksch T, Heine A, Klebe G, Diederich WE. Achiral oligoamines as versatile tool for the development of aspartic protease inhibitors. Bioorg Med Chem 2008; 16:8574-86. [DOI: 10.1016/j.bmc.2008.08.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 07/29/2008] [Accepted: 08/04/2008] [Indexed: 10/21/2022]
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39
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Zürcher M, Diederich F. Structure-Based Drug Design: Exploring the Proper Filling of Apolar Pockets at Enzyme Active Sites. J Org Chem 2008; 73:4345-61. [DOI: 10.1021/jo800527n] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martina Zürcher
- Department of Chemistry and Applied Biosciences, Laboratorium für Organische Chemie, ETH Zürich, HCI G 313, 8093 Zürich, Switzerland
| | - François Diederich
- Department of Chemistry and Applied Biosciences, Laboratorium für Organische Chemie, ETH Zürich, HCI G 313, 8093 Zürich, Switzerland
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Yokokawa F, Maibaum J. Recent advances in the discovery of non-peptidic direct renin inhibitors as antihypertensives: new patent applications in years 2000 – 2008. Expert Opin Ther Pat 2008. [DOI: 10.1517/13543776.18.6.581] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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41
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Zürcher M, Gottschalk T, Meyer S, Bur D, Diederich F. Exploring the Flap Pocket of the Antimalarial Target Plasmepsin II: The “55 % Rule” Applied to Enzymes. ChemMedChem 2008; 3:237-40. [DOI: 10.1002/cmdc.200700236] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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43
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Ersmark K, Samuelsson B, Hallberg A. Plasmepsins as potential targets for new antimalarial therapy. Med Res Rev 2007; 26:626-66. [PMID: 16838300 DOI: 10.1002/med.20082] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Malaria is one of the major diseases in the world. Due to the rapid spread of parasite resistance to available antimalarial drugs there is an urgent need for new antimalarials with novel mechanisms of action. Several promising targets for drug intervention have been revealed in recent years. This review addresses the parasitic aspartic proteases termed plasmepsins (Plms) that are involved in the hemoglobin catabolism that occurs during the erythrocytic stage of the malarial parasite life cycle. Four Plasmodium species are responsible for human malaria; P. vivax, P. ovale, P. malariae, and P. falciparum. This review focuses on inhibitors of the haemoglobin-degrading plasmepsins of the most lethal species, P. falciparum; Plm I, Plm II, Plm IV, and histo-aspartic protease (HAP). Previously, Plm II has attracted the most attention. With the identification and characterization of new plasmepsins and the results from recent plasmepsin knockout studies, it now seems clear that in order to achieve high-antiparasitic activities in P. falciparum-infected erythrocytes it is necessary to inhibit several of the haemoglobin-degrading plasmepsins. Herein we summarize the structure-activity relationships of the Plm I, II, IV, and HAP inhibitors. These inhibitors represent all classes which, to the best of our knowledge, have been disclosed in journal articles to date. The 3D structures of inhibitor/plasmepsin II complexes available in the protein data bank are briefly discussed and compared.
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Affiliation(s)
- Karolina Ersmark
- Department of Medicinal Chemistry, Uppsala University, BMC, SE-751 23 Uppsala, Sweden
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44
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Maibaum J, Stutz S, Göschke R, Rigollier P, Yamaguchi Y, Cumin F, Rahuel J, Baum HP, Cohen NC, Schnell CR, Fuhrer W, Gruetter MG, Schilling W, Wood JM. Structural modification of the P2' position of 2,7-dialkyl-substituted 5(S)-amino-4(S)-hydroxy-8-phenyl-octanecarboxamides: the discovery of aliskiren, a potent nonpeptide human renin inhibitor active after once daily dosing in marmosets. J Med Chem 2007; 50:4832-44. [PMID: 17824680 DOI: 10.1021/jm070316i] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Due to its function in the rate limiting initial step of the renin-angiotensin system, renin is a particularly promising target for drugs designed to control hypertension, a growing risk to health worldwide. Despite vast efforts over more than two decades, no orally efficacious renin inhibitor had reached the market. As a result of a structure-based topological design approach, we have identified a novel class of small-molecule inhibitors with good oral blood-pressure lowering effects in primates. Further lead optimization aimed for improvement of in vivo potency and duration of action, mainly by P2' modifications at the hydroxyethylene transition-state isostere. These efforts resulted in the discovery of aliskiren (46, CGP060536B, SPP100), a highly potent, selective inhibitor of renin, demonstrating excellent efficacy in sodium-depleted marmosets after oral administration, with sustained duration of action in reducing dose-dependently mean arterial blood pressure. Aliskiren has recently received regulatory approval by the U.S. Food and Drug Administration for the treatment of hypertension.
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Affiliation(s)
- Jürgen Maibaum
- Novartis Institutes for BioMedical Research, NOVARTIS Pharma AG, WKL-136.683, CH-4002 Basel, Switzerland.
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45
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Powell NA, Ciske FL, Cai C, Holsworth DD, Mennen K, Van Huis CA, Jalaie M, Day J, Mastronardi M, McConnell P, Mochalkin I, Zhang E, Ryan MJ, Bryant J, Collard W, Ferreira S, Gu C, Collins R, Edmunds JJ. Rational design of 6-(2,4-diaminopyrimidinyl)-1,4-benzoxazin-3-ones as small molecule renin inhibitors. Bioorg Med Chem 2007; 15:5912-49. [PMID: 17574423 DOI: 10.1016/j.bmc.2007.05.069] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Revised: 05/25/2007] [Accepted: 05/29/2007] [Indexed: 10/23/2022]
Abstract
We report the design and synthesis of a series of 6-(2,4-diaminopyrimidinyl)-1,4-benzoxazin-3-ones as orally bioavailable small molecule inhibitors of renin. Compounds with a 2-methyl-2-aryl substitution pattern exhibit potent renin inhibition and good permeability, solubility, and metabolic stability. Oral bioavailability was found to be dependent on metabolic clearance and cellular permeability, and was optimized through modulation of the sidechain that binds in the S3(sp) subsite.
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Affiliation(s)
- Noel A Powell
- Pfizer Global Research & Development, Michigan Laboratories, Ann Arbor, MI 48105, USA.
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46
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Holsworth DD, Jalaie M, Belliotti T, Cai C, Collard W, Ferreira S, Powell NA, Stier M, Zhang E, McConnell P, Mochalkin I, Ryan MJ, Bryant J, Li T, Kasani A, Subedi R, Maiti SN, Edmunds JJ. Discovery of 6-ethyl-2,4-diaminopyrimidine-based small molecule renin inhibitors. Bioorg Med Chem Lett 2007; 17:3575-80. [DOI: 10.1016/j.bmcl.2007.04.052] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Revised: 04/17/2007] [Accepted: 04/18/2007] [Indexed: 11/30/2022]
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47
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Ekins S, Mestres J, Testa B. In silico pharmacology for drug discovery: applications to targets and beyond. Br J Pharmacol 2007; 152:21-37. [PMID: 17549046 PMCID: PMC1978280 DOI: 10.1038/sj.bjp.0707306] [Citation(s) in RCA: 202] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Computational (in silico) methods have been developed and widely applied to pharmacology hypothesis development and testing. These in silico methods include databases, quantitative structure-activity relationships, similarity searching, pharmacophores, homology models and other molecular modeling, machine learning, data mining, network analysis tools and data analysis tools that use a computer. Such methods have seen frequent use in the discovery and optimization of novel molecules with affinity to a target, the clarification of absorption, distribution, metabolism, excretion and toxicity properties as well as physicochemical characterization. The first part of this review discussed the methods that have been used for virtual ligand and target-based screening and profiling to predict biological activity. The aim of this second part of the review is to illustrate some of the varied applications of in silico methods for pharmacology in terms of the targets addressed. We will also discuss some of the advantages and disadvantages of in silico methods with respect to in vitro and in vivo methods for pharmacology research. Our conclusion is that the in silico pharmacology paradigm is ongoing and presents a rich array of opportunities that will assist in expediating the discovery of new targets, and ultimately lead to compounds with predicted biological activity for these novel targets.
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Affiliation(s)
- S Ekins
- ACT LLC, 1 Penn Plaza, New York, NY 10119, USA.
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48
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Murray CW, Callaghan O, Chessari G, Cleasby A, Congreve M, Frederickson M, Hartshorn MJ, McMenamin R, Patel S, Wallis N. Application of fragment screening by X-ray crystallography to beta-secretase. J Med Chem 2007; 50:1116-23. [PMID: 17315856 DOI: 10.1021/jm0611962] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper describes an application of fragment screening to the aspartyl protease enzyme, beta-secretase (BACE-1), using high throughput X-ray crystallography. Three distinct chemotypes were identified by X-ray crystallography as binding to the catalytic aspartates either via an aminoheterocycle (such as 2-aminoquinoline), a piperidine, or an aliphatic hydroxyl group. The fragment hits were weak inhibitors of BACE-1 in the millimolar range but were of interest because most of them displayed relatively good ligand efficiencies. The aminoheterocycles exhibited a novel recognition motif that has not been seen before with aspartic proteases. Virtual screening around this motif identified an aminopyridine with increased potency and attractive growth points for further elaboration using structure-based drug design. The companion paper illustrates how sub-micromolar inhibitors were developed starting from this fragment.
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Affiliation(s)
- Christopher W Murray
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom.
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49
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Congreve M, Aharony D, Albert J, Callaghan O, Campbell J, Carr RAE, Chessari G, Cowan S, Edwards PD, Frederickson M, McMenamin R, Murray CW, Patel S, Wallis N. Application of Fragment Screening by X-ray Crystallography to the Discovery of Aminopyridines as Inhibitors of β-Secretase. J Med Chem 2007; 50:1124-32. [PMID: 17315857 DOI: 10.1021/jm061197u] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fragment-based lead discovery has been successfully applied to the aspartyl protease enzyme beta-secretase (BACE-1). Fragment hits that contained an aminopyridine motif binding to the two catalytic aspartic acid residues in the active site of the enzyme were the chemical starting points. Structure-based design approaches have led to identification of low micromolar lead compounds that retain these interactions and additionally occupy adjacent hydrophobic pockets of the active site. These leads form two subseries, for which compounds 4 (IC50 = 25 microM) and 6c (IC50 = 24 microM) are representative. In the latter series, further optimization has led to 8a (IC50 = 690 nM).
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Affiliation(s)
- Miles Congreve
- Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom.
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50
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Bower JF, Riis-Johannessen T, Szeto P, Whitehead AJ, Gallagher T. Stereospecific construction of substituted piperidines. Synthesis of (−)-paroxetine and (+)-laccarin. Chem Commun (Camb) 2007:728-30. [PMID: 17392964 DOI: 10.1039/b617260a] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Short and efficient enantioselective syntheses of (-)-paroxetine and (+)-laccarin are described based on the highly stereospecific cleavage of C(3)-substituted 1,3-cyclic sulfamidates.
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Affiliation(s)
- John F Bower
- School of Chemistry, University of Bristol, Bristol, UKBS8 1TS
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