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Verma M, Trivedi L, Vasudev PG. Interaction Patterns of Pyrazolopyrimidines with Receptor Proteins. J Chem Inf Model 2023; 63:2331-2344. [PMID: 37023262 DOI: 10.1021/acs.jcim.2c01315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Heterocyclic compounds have a prominent role in medicinal chemistry and drug design. They are not only useful as medicinally active compounds but also as a modular structural scaffold for drug design. Therefore, heterocycles are present in many ligands that exhibit a broad spectrum of biological activities. Pyazolopyrimidines are nitrogen heterocycles and are part of many biologically active compounds and marketed drugs. This study examines the non-covalent interactions between the pyrazolopyrimidine rings and receptor proteins through data mining and analysis of high-resolution crystal structures deposited in the Protein Data Bank. The Protein Data Bank contains 471 crystal structures with pyrazolopyrimidine derivatives as ligands, among which 50% contains 1H-pyrazolo[3,4-d]pyrimidines (Pyp1), while 38% contains pyrazolo[1,5-a] pyrimidines (Pyp2). 1H-Pyrazolo[4,3-d]pyrimidines (Pyp3) are found in 11% of the structures, and no structural data is available for pyrazolo[1,5-c]pyrimidine isomers (Pyp4). Among receptor proteins, transferases are found in most examples (67.5%), followed by hydrolases (13.4%) and oxidoreductases (8.9%). Detailed analysis of structures to identify the most prevalent interactions of pyrazolopyrimidines with proteins shows that aromatic π···π interactions are present in ∼91% of the structures and hydrogen bonds/other polar contacts are present in ∼73% of the structures. The centroid-centroid distances (dcent) between the pyrazolopyrimidine rings and aromatic side chains of the proteins have been retrieved from crystal structures recorded at a high resolution (data resolution <2.0 Å). The average value of dcent in pyrazolopyrimidine-protein complexes is 5.32 Å. The information on the geometric parameters of aromatic interactions between the core pyrazolopyrimidine ring and the protein would be helpful in future in silico modeling studies on pyrazolopyrimidine-receptor complexes.
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Affiliation(s)
- Meenakshi Verma
- Plant Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 220025, India
| | - Laxmikant Trivedi
- Plant Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India
| | - Prema G Vasudev
- Plant Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 220025, India
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2
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Morriello GJ, Dwyer MP, Chen Y, Ginetti AT, Xu S, Lu J, Abeywickrema P, Wang D, Crespo A, Cabalu TD, Wilson JE, Stachel SJ, Paone DV, Sinz C. Discovery of novel N-1 substituted pyrazolopyrimidinones as potent, selective PDE2 inhibitors. Bioorg Med Chem Lett 2021; 44:128082. [PMID: 33991626 DOI: 10.1016/j.bmcl.2021.128082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022]
Abstract
A focused SAR study was conducted on a series of N1-substituted pyrazolopyrimidinone PDE2 inhibitors to reveal compounds with excellent potency and selectivity. The series was derived from previously identified internal leads and designed to enhance steric interactions with key amino acids in the PDE2 binding pocket. Compound 26 was identified as a lead compound with excellent PDE2 selectivity and good physicochemical properties.
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Affiliation(s)
- Gregori J Morriello
- Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Rd., Kenilworth, NJ 07033, USA.
| | - Michael P Dwyer
- Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Rd., Kenilworth, NJ 07033, USA
| | - Yili Chen
- Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Rd., Kenilworth, NJ 07033, USA
| | - Anthony T Ginetti
- Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Rd., Kenilworth, NJ 07033, USA
| | - Shimin Xu
- Discovery Chemistry, Merck & Co., Inc., 2000 Galloping Hill Rd., Kenilworth, NJ 07033, USA
| | - Jun Lu
- Discovery Chemistry, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
| | - Pravien Abeywickrema
- Discovery Chemistry, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
| | - Deping Wang
- Discovery Chemistry, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
| | - Alejandro Crespo
- Discovery Chemistry, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
| | - Tamara D Cabalu
- Drug Metabolism, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
| | - Jonathan E Wilson
- Discovery Chemistry, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
| | - Shawn J Stachel
- Discovery Chemistry, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
| | - Daniel V Paone
- Discovery Chemistry, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA
| | - Christopher Sinz
- Discovery Chemistry, Merck & Co., Inc., 213 E. Grand Avenue, South San Fransisco, CA 94080, USA
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Bauer MR, Di Fruscia P, Lucas SCC, Michaelides IN, Nelson JE, Storer RI, Whitehurst BC. Put a ring on it: application of small aliphatic rings in medicinal chemistry. RSC Med Chem 2021; 12:448-471. [PMID: 33937776 PMCID: PMC8083977 DOI: 10.1039/d0md00370k] [Citation(s) in RCA: 149] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/18/2020] [Indexed: 12/15/2022] Open
Abstract
Aliphatic three- and four-membered rings including cyclopropanes, cyclobutanes, oxetanes, azetidines and bicyclo[1.1.1]pentanes have been increasingly exploited in medicinal chemistry for their beneficial physicochemical properties and applications as functional group bioisosteres. This review provides a historical perspective and comparative up to date overview of commonly applied small rings, exemplifying key principles with recent literature examples. In addition to describing the merits and advantages of each ring system, potential hazards and liabilities are also illustrated and explained, including any significant chemical or metabolic stability and toxicity risks.
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Affiliation(s)
- Matthias R Bauer
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | - Paolo Di Fruscia
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | - Simon C C Lucas
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | | | - Jennifer E Nelson
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | - R Ian Storer
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
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4
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Nadur NF, de Azevedo LL, Caruso L, Graebin CS, Lacerda RB, Kümmerle AE. The long and winding road of designing phosphodiesterase inhibitors for the treatment of heart failure. Eur J Med Chem 2020; 212:113123. [PMID: 33412421 DOI: 10.1016/j.ejmech.2020.113123] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 12/14/2022]
Abstract
Cyclic nucleotide phosphodiesterases (PDEs) are a superfamily of enzymes known to play a critical role in the indirect regulation of several intracellular metabolism pathways through the selective hydrolysis of the phosphodiester bonds of specific second messenger substrates such as cAMP (3',5'-cyclic adenosine monophosphate) and cGMP (3',5'-cyclic guanosine monophosphate), influencing the hypertrophy, contractility, apoptosis and fibroses in the cardiovascular system. The expression and/or activity of multiple PDEs is altered during heart failure (HF), which leads to changes in levels of cyclic nucleotides and function of cardiac muscle. Within the cardiovascular system, PDEs 1-5, 8 and 9 are expressed and are interesting targets for the HF treatment. In this comprehensive review we will present a briefly description of the biochemical importance of each cardiovascular related PDE to the HF, and cover almost all the "long and winding road" of designing and discovering ligands, hits, lead compounds, clinical candidates and drugs as PDE inhibitors in the last decade.
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Affiliation(s)
- Nathalia Fonseca Nadur
- Laboratório de Diversidade Molecular e Química Medicinal (LaDMol-QM, Molecular Diversity and Medicinal Chemistry Laboratory), Chemistry Institute, Rural Federal University of Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil; Programa de Pós-Gradução em Química (PPGQ), Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
| | - Luciana Luiz de Azevedo
- Laboratório de Diversidade Molecular e Química Medicinal (LaDMol-QM, Molecular Diversity and Medicinal Chemistry Laboratory), Chemistry Institute, Rural Federal University of Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil; Programa de Pós-Gradução em Química (PPGQ), Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
| | - Lucas Caruso
- Laboratório de Diversidade Molecular e Química Medicinal (LaDMol-QM, Molecular Diversity and Medicinal Chemistry Laboratory), Chemistry Institute, Rural Federal University of Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil; Programa de Pós-Gradução em Química (PPGQ), Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
| | - Cedric Stephan Graebin
- Laboratório de Diversidade Molecular e Química Medicinal (LaDMol-QM, Molecular Diversity and Medicinal Chemistry Laboratory), Chemistry Institute, Rural Federal University of Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil; Programa de Pós-Gradução em Química (PPGQ), Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
| | - Renata Barbosa Lacerda
- Programa de Pós-Gradução em Química (PPGQ), Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil
| | - Arthur Eugen Kümmerle
- Laboratório de Diversidade Molecular e Química Medicinal (LaDMol-QM, Molecular Diversity and Medicinal Chemistry Laboratory), Chemistry Institute, Rural Federal University of Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil; Programa de Pós-Gradução em Química (PPGQ), Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-000, Brazil.
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5
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Fragments: where are we now? Biochem Soc Trans 2020; 48:271-280. [PMID: 31985743 DOI: 10.1042/bst20190694] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 12/30/2022]
Abstract
Fragment-based drug discovery (FBDD) has become a mainstream technology for the identification of chemical hit matter in drug discovery programs. To date, the food and drug administration has approved four drugs, and over forty compounds are in clinical studies that can trace their origins to a fragment-based screen. The challenges associated with implementing an FBDD approach are many and diverse, ranging from the library design to developing methods for identifying weak affinity compounds. In this article, we give an overview of current progress in fragment library design, fragment to lead optimisation and on the advancement in techniques used for screening. Finally, we will comment on the future opportunities and challenges in this field.
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Majewski M, Ruiz-Carmona S, Barril X. An investigation of structural stability in protein-ligand complexes reveals the balance between order and disorder. Commun Chem 2019. [DOI: 10.1038/s42004-019-0205-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
The predominant view in structure-based drug design is that small-molecule ligands, once bound to their target structures, display a well-defined binding mode. However, structural stability (robustness) is not necessary for thermodynamic stability (binding affinity). In fact, it entails an entropic penalty that counters complex formation. Surprisingly, little is known about the causes, consequences and real degree of robustness of protein-ligand complexes. Since hydrogen bonds have been described as essential for structural stability, here we investigate 469 such interactions across two diverse structure sets, comprising of 79 drug-like and 27 fragment ligands, respectively. Completely constricted protein-ligand complexes are rare and may fulfill a functional role. Most complexes balance order and disorder by combining a single anchoring point with looser regions. 25% do not contain any robust hydrogen bond and may form loose structures. Structural stability analysis reveals a hidden layer of complexity in protein-ligand complexes that should be considered in ligand design.
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7
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Sharma P, Srivastava P, Seth A, Tripathi PN, Banerjee AG, Shrivastava SK. Comprehensive review of mechanisms of pathogenesis involved in Alzheimer's disease and potential therapeutic strategies. Prog Neurobiol 2018; 174:53-89. [PMID: 30599179 DOI: 10.1016/j.pneurobio.2018.12.006] [Citation(s) in RCA: 202] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 12/04/2018] [Accepted: 12/28/2018] [Indexed: 12/14/2022]
Abstract
AD is a progressive neurodegenerative disorder and a leading cause of dementia in an aging population worldwide. The enormous challenge which AD possesses to global healthcare makes it as urgent as ever for the researchers to develop innovative treatment strategies to fight this disease. An in-depth analysis of the extensive available data associated with the AD is needed for a more comprehensive understanding of underlying molecular mechanisms and pathophysiological pathways associated with the onset and progression of the AD. The currently understood pathological and biochemical manifestations include cholinergic, Aβ, tau, excitotoxicity, oxidative stress, ApoE, CREB signaling pathways, insulin resistance, etc. However, these hypotheses have been criticized with several conflicting reports for their involvement in the disease progression. Several issues need to be addressed such as benefits to cost ratio with cholinesterase therapy, the dilemma of AChE selectivity over BChE, BBB permeability of peptidic BACE-1 inhibitors, hurdles related to the implementation of vaccination and immunization therapy, and clinical failure of candidates related to newly available targets. The present review provides an insight to the different molecular mechanisms involved in the development and progression of the AD and potential therapeutic strategies, enlightening perceptions into structural information of conventional and novel targets along with the successful applications of computational approaches for the design of target-specific inhibitors.
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Affiliation(s)
- Piyoosh Sharma
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Pavan Srivastava
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Ankit Seth
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Prabhash Nath Tripathi
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Anupam G Banerjee
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Sushant K Shrivastava
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India.
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8
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Mortenson PN, Erlanson DA, de Esch IJP, Jahnke W, Johnson CN. Fragment-to-Lead Medicinal Chemistry Publications in 2017. J Med Chem 2018; 62:3857-3872. [PMID: 30462504 DOI: 10.1021/acs.jmedchem.8b01472] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This Miniperspective is the third in a series reviewing fragment-to-lead publications from a given year. Following our reviews for 2015 and 2016, this Miniperspective provides tabulated summaries of relevant articles published in 2017 along with some general observations. In addition, we discuss insights obtained from analysis of the combined data set of 85 examples from all three years of publications.
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Affiliation(s)
- Paul N Mortenson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
| | - Daniel A Erlanson
- Carmot Therapeutics Inc. , 740 Heinz Avenue , Berkeley , California 94710 , United States
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ , Amsterdam , The Netherlands
| | - Wolfgang Jahnke
- Chemical Biology and Therapeutics , Novartis Institutes for Biomedical Research , 4002 Basel , Switzerland
| | - Christopher N Johnson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
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9
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Bi XA, Xu Q, Luo X, Sun Q, Wang Z. Analysis of Progression Toward Alzheimer's Disease Based on Evolutionary Weighted Random Support Vector Machine Cluster. Front Neurosci 2018; 12:716. [PMID: 30349454 PMCID: PMC6186825 DOI: 10.3389/fnins.2018.00716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 09/19/2018] [Indexed: 12/02/2022] Open
Abstract
Alzheimer’s disease (AD) could be described into following four stages: healthy control (HC), early mild cognitive impairment (EMCI), late MCI (LMCI) and AD dementia. The discriminations between different stages of AD are considerably important issues for future pre-dementia treatment. However, it is still challenging to identify LMCI from EMCI because of the subtle changes in imaging which are not noticeable. In addition, there were relatively few studies to make inferences about the brain dynamic changes in the cognitive progression from EMCI to LMCI to AD. Inspired by the above problems, we proposed an advanced approach of evolutionary weighted random support vector machine cluster (EWRSVMC). Where the predictions of numerous weighted SVM classifiers are aggregated for improving the generalization performance. We validated our method in multiple binary classifications using Alzheimer’s Disease Neuroimaging Initiative dataset. As a result, the encouraging accuracy of 90% for EMCI/LMCI and 88.89% for LMCI/AD were achieved respectively, demonstrating the excellent discriminating ability. Furthermore, disease-related brain regions underlying the AD progression could be found out on the basis of the amount of discriminative information. The findings of this study provide considerable insight into the neurophysiological mechanisms in AD development.
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Affiliation(s)
- Xia-An Bi
- College of Information Science and Engineering, Hunan Normal University, Changsha, China
| | - Qian Xu
- College of Information Science and Engineering, Hunan Normal University, Changsha, China
| | - Xianhao Luo
- College of Mathematics and Statistics, Hunan Normal University, Changsha, China
| | - Qi Sun
- College of Information Science and Engineering, Hunan Normal University, Changsha, China
| | - Zhigang Wang
- College of Information Science and Engineering, Hunan Normal University, Changsha, China
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Stachel SJ, Berger R, Nomland AB, Ginnetti AT, Paone DV, Wang D, Puri V, Lange H, Drott J, Lu J, Marcus J, Dwyer MP, Suon S, Uslaner JM, Smith SM. Structure-Guided Design and Procognitive Assessment of a Potent and Selective Phosphodiesterase 2A Inhibitor. ACS Med Chem Lett 2018; 9:815-820. [PMID: 30128073 DOI: 10.1021/acsmedchemlett.8b00214] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/26/2018] [Indexed: 12/20/2022] Open
Abstract
Herein we describe the development of a series of pyrazolopyrimidinone phosphodiesterase 2A (PDE2) inhibitors using structure-guided lead identification and design. The series was derived from informed chemotype replacement based on previously identified internal leads. The initially designed compound 3, while potent on PDE2, displayed unsatisfactory selectivity against the other PDE2 isoforms. Compound 3 was subsequently optimized for improved PDE2 activity and isoform selectivity. Insights into the origins of PDE2 selectivity are described and verified using cocrystallography. An optimized lead, 4, demonstrated improved performance in both a rodent and a nonhuman primate cognition model.
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Affiliation(s)
- Shawn J. Stachel
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Richard Berger
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Ashley B. Nomland
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | | | - Daniel V. Paone
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Deping Wang
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Vanita Puri
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Henry Lange
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Jason Drott
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Jun Lu
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Jacob Marcus
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Michael P. Dwyer
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Sokreine Suon
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Jason M. Uslaner
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
| | - Sean M. Smith
- Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States
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