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Shah HS, Michelle C, Xie T, Chaturvedi K, Kuang S, Abramov YA. Computational and Experimental Screening Approaches to Aripiprazole Salt Crystallization. Pharm Res 2023; 40:2779-2789. [PMID: 37127778 DOI: 10.1007/s11095-023-03522-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
INTRODUCTION The screening of multicomponent crystal system (MCC) is a key method for improving physicochemical properties of active pharmaceutical ingredients (APIs). The challenges associated with experimental salt screening include a large number of potential counterions and solvent systems and tendency to undergo disproportionation to produce free form during crystallization. These challenges may be mitigated by a combination of experimental and computational approaches to salt screening. The goal of this study is to evaluate performance of the counterion screening methods and propose and validate novel approaches to virtual solvent screening for MCC crystallization. METHODS The actual performance of the ΔpKa > 3 rule for counterion selection was validated using multiple screenings reports. Novel computational models for virtual solvent screening to avoid MCC incongruent crystallization were proposed. Using the ΔpKa rule, 10 acid counterions were selected for experimental aripiprazole (APZ) salt screening using 10 organic solvents. The experimental results were used to validate the proposed novel virtual solvent screen models. RESULTS Experimental APZ salt screening resulted in a total of eight MCCs which included glucuronate, mesylate, oxalate, tartrate, salicylate and mandelate. The new model to virtually screen solvents provided a general agreement with APZ experimental findings in terms of selecting the optimal solvent for MCC crystallization. CONCLUSION The rational selection of counterions and organic solvents for MCC crystallization was presented using combined novel computational model as well as experimental studies. The current virtual solvent screen model was successfully implemented and validated which can be easily applied to newly discovered APIs.
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Affiliation(s)
- Harsh S Shah
- J-Star Research Inc., 6 Cedarbrook Drive, Cranbury, NJ, 08512, USA.
| | | | - Tian Xie
- J-Star Research Inc., 6 Cedarbrook Drive, Cranbury, NJ, 08512, USA
| | | | - Shanming Kuang
- J-Star Research Inc., 6 Cedarbrook Drive, Cranbury, NJ, 08512, USA
| | - Yuriy A Abramov
- J-Star Research Inc., 6 Cedarbrook Drive, Cranbury, NJ, 08512, USA.
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.
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Abramov YA, Iuzzolino L, Jin Y, York G, Chen CH, Shultz CS, Yang Z, Chang C, Shi B, Zhou T, Greenwell C, Sekharan S, Lee AY. Cocrystal Synthesis through Crystal Structure Prediction. Mol Pharm 2023. [PMID: 37279175 DOI: 10.1021/acs.molpharmaceut.2c01098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Crystal structure prediction (CSP) is an invaluable tool in the pharmaceutical industry because it allows to predict all the possible crystalline solid forms of small-molecule active pharmaceutical ingredients. We have used a CSP-based cocrystal prediction method to rank ten potential cocrystal coformers by the energy of the cocrystallization reaction with an antiviral drug candidate, MK-8876, and a triol process intermediate, 2-ethynylglyclerol. For MK-8876, the CSP-based cocrystal prediction was performed retrospectively and successfully predicted the maleic acid cocrystal as the most likely cocrystal to be observed. The triol is known to form two different cocrystals with 1,4-diazabicyclo[2.2.2]octane (DABCO), but a larger solid form landscape was desired. CSP-based cocrystal screening predicted the triol-DABCO cocrystal as rank one, while a triol-l-proline cocrystal was predicted as rank two. Computational finite-temperature corrections enabled determination of relative crystallization propensities of the triol-DABCO cocrystals with different stoichiometries and prediction of the triol-l-proline polymorphs in the free-energy landscape. The triol-l-proline cocrystal was obtained during subsequent targeted cocrystallization experiments and was found to exhibit an improved melting point and deliquescence behavior over the triol-free acid, which could be considered as an alternative solid form in the synthesis of islatravir.
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Affiliation(s)
- Yuriy A Abramov
- XtalPi Inc., 245 Main Street, Cambridge, Massachusetts 02142, United States
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Luca Iuzzolino
- Computational and Structural Chemistry, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Yingdi Jin
- XtalPi, Inc., Shenzhen Jingtai Technology Co., Ltd., Futian District, Shenzhen 518100, China
| | - Gregory York
- Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Chien-Hung Chen
- Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - C Scott Shultz
- Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Zhuocen Yang
- XtalPi, Inc., Shenzhen Jingtai Technology Co., Ltd., Futian District, Shenzhen 518100, China
| | - Chao Chang
- XtalPi, Inc., Shenzhen Jingtai Technology Co., Ltd., Futian District, Shenzhen 518100, China
| | - Baimei Shi
- XtalPi, Inc., Shenzhen Jingtai Technology Co., Ltd., Futian District, Shenzhen 518100, China
| | - Tian Zhou
- XtalPi, Inc., Shenzhen Jingtai Technology Co., Ltd., Futian District, Shenzhen 518100, China
| | - Chandler Greenwell
- XtalPi Inc., 245 Main Street, Cambridge, Massachusetts 02142, United States
| | - Sivakumar Sekharan
- XtalPi Inc., 245 Main Street, Cambridge, Massachusetts 02142, United States
| | - Alfred Y Lee
- Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
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Abstract
Computational chemistry applications have become an integral part of the drug discovery workflow over the past 35 years. However, computational modeling in support of drug development has remained a relatively uncharted territory for a significant part of both academic and industrial communities. This review considers the computational modeling workflows for three key components of drug preclinical and clinical development, namely, process chemistry, analytical research and development, as well as drug product and formulation development. An overview of the computational support for each step of the respective workflows is presented. Additionally, in context of solid form design, special consideration is given to modern physics-based virtual screening methods. This covers rational approaches to polymorph, coformer, counterion, and solvent virtual screening in support of solid form selection and design.
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Affiliation(s)
- Yuriy A Abramov
- XtalPi, Inc., 245 Main St., Cambridge, Massachusetts 02142, United States.,Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Guangxu Sun
- XtalPi, Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 3, Sf Industrial Plant, No. 2 Hongliu road, Fubao Community, Fubao Street, Futian District, Shenzhen 518100, China
| | - Qun Zeng
- XtalPi, Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 3, Sf Industrial Plant, No. 2 Hongliu road, Fubao Community, Fubao Street, Futian District, Shenzhen 518100, China
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Yuan J, Liu X, Wang S, Chang C, Zeng Q, Song Z, Jin Y, Zeng Q, Sun G, Ruan S, Greenwell C, Abramov YA. Virtual coformer screening by a combined machine learning and physics-based approach. CrystEngComm 2021. [DOI: 10.1039/d1ce00587a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Cocrystals as a solid form technology for improving physicochemical properties have gained increasing popularity in the pharmaceutical, nutraceutical, and agrochemical industries.
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Affiliation(s)
- Jiuchuang Yuan
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 3, Sf Industrial Plant, No. 2 hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen, 518100 China
| | - Xuetao Liu
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 3, Sf Industrial Plant, No. 2 hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen, 518100 China
- Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogeomics, Peking University Shenzhen Graduate School, Shenzhen, 518055 China
| | - Simin Wang
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 3, Sf Industrial Plant, No. 2 hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen, 518100 China
| | - Chao Chang
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 3, Sf Industrial Plant, No. 2 hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen, 518100 China
| | - Qiao Zeng
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 3, Sf Industrial Plant, No. 2 hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen, 518100 China
| | - Zhengtian Song
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 3, Sf Industrial Plant, No. 2 hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen, 518100 China
| | - Yingdi Jin
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 3, Sf Industrial Plant, No. 2 hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen, 518100 China
| | - Qun Zeng
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 3, Sf Industrial Plant, No. 2 hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen, 518100 China
| | - Guangxu Sun
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 3, Sf Industrial Plant, No. 2 hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen, 518100 China
| | - Shigang Ruan
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 3, Sf Industrial Plant, No. 2 hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen, 518100 China
| | | | - Yuriy A. Abramov
- XtalPi Inc, Cambridge, Massachusetts 02142, USA
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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Sun G, Jin Y, Li S, Yang Z, Shi B, Chang C, Abramov YA. Virtual Coformer Screening by Crystal Structure Predictions: Crucial Role of Crystallinity in Pharmaceutical Cocrystallization. J Phys Chem Lett 2020; 11:8832-8838. [PMID: 32969658 DOI: 10.1021/acs.jpclett.0c02371] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
One of the most popular strategies of the optimization of drug properties in the pharmaceutical industry appears to be a solid form changing into a cocrystalline form. A number of virtual screening approaches have been previously developed to allow a selection of the most promising cocrystal formers (coformers) for an experimental follow-up. A significant drawback of those methods is related to the lack of accounting for the crystallinity contribution to cocrystal formation. To address this issue, we propose in this study two virtual coformer screening approaches based on a modern cloud-computing crystal structure prediction (CSP) technology at a dispersion-corrected density functional theory (DFT-D) level. The CSP-based methods were for the first time validated on challenging cases of indomethacin and paracetamol cocrystallization, for which the previously developed approaches provided poor predictions. The calculations demonstrated a dramatic improvement of the virtual coformer screening performance relative to the other methods. It is demonstrated that the crystallinity contribution to the formation of paracetamol and indomethacin cocrystals is a dominant one and, therefore, should not be ignored in the virtual screening calculations. Our results encourage a broad utilization of the proposed CSP-based technology in the pharmaceutical industry as the only virtual coformer screening method that directly accounts for the crystallinity contribution.
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Affiliation(s)
- Guangxu Sun
- XtalPi Inc. (Shenzhen Jingtai Technology Co., Ltd.), Floor 4, No. 9, Hualian Industrial Zone, Dalang Street, Longhua District, Shenzhen 518100, China
| | - Yingdi Jin
- XtalPi Inc. (Shenzhen Jingtai Technology Co., Ltd.), Floor 4, No. 9, Hualian Industrial Zone, Dalang Street, Longhua District, Shenzhen 518100, China
| | - Sizhu Li
- XtalPi Inc. (Shenzhen Jingtai Technology Co., Ltd.), Floor 4, No. 9, Hualian Industrial Zone, Dalang Street, Longhua District, Shenzhen 518100, China
| | - Zhuocen Yang
- XtalPi Inc. (Shenzhen Jingtai Technology Co., Ltd.), Floor 4, No. 9, Hualian Industrial Zone, Dalang Street, Longhua District, Shenzhen 518100, China
| | - Baimei Shi
- XtalPi Inc. (Shenzhen Jingtai Technology Co., Ltd.), Floor 4, No. 9, Hualian Industrial Zone, Dalang Street, Longhua District, Shenzhen 518100, China
| | - Chao Chang
- XtalPi Inc. (Shenzhen Jingtai Technology Co., Ltd.), Floor 4, No. 9, Hualian Industrial Zone, Dalang Street, Longhua District, Shenzhen 518100, China
| | - Yuriy A Abramov
- XtalPi Inc, 245 Main Street, Cambridge, Massachusetts 02142, United States
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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6
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Affiliation(s)
- Yuriy A. Abramov
- XtalPi Inc, 245 Main Street, Cambridge, Massachusetts 02142, United States
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Guangxu Sun
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 4, No. 9, Hualian Industrial Zone, Dalang Street, Longhua District, Shenzhen 518100, China
| | - Qiao Zeng
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 4, No. 9, Hualian Industrial Zone, Dalang Street, Longhua District, Shenzhen 518100, China
| | - Qun Zeng
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 4, No. 9, Hualian Industrial Zone, Dalang Street, Longhua District, Shenzhen 518100, China
| | - Mingjun Yang
- XtalPi Inc., Shenzhen Jingtai Technology Co., Ltd., Floor 4, No. 9, Hualian Industrial Zone, Dalang Street, Longhua District, Shenzhen 518100, China
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Abstract
Accurate crystal structures and their experimental uncertainties, determined by X-ray diffraction/neutron diffraction techniques, are vital for crystal engineering studies, such as polymorph stability and crystal morphology calculations. Because of differences in crystal growth and data measurement conditions, crystallographic databases often contain multiple entries of varying quality of the same compound. The choice of the most reliable and best quality crystal structure from many very similar structures remains an unresolved problem, especially for nonexperts. In addition, while crystallographers can make use of some professional software (i.e., Materials Studio) for structure refinement, noncrystallographers may not have access to it. In the present paper, we propose a simple method to study the sensitivity of the crystal lattice energy to changes in the structural parameters, which creates a diagnostic tool to test the quality of crystal structure files and to improve the low-quality structures based on lattice energy distribution. Thus, noncrystallographers could take the proposed idea and program/optimize crystal structure by themselves. They can have their in-house program to determine the reliability of the selected crystal data and then use the best quality data or carry out structural optimization for low-quality data. The proposed method will benefit a broad cross-section of scientific researchers, especially those in solid-state and physical chemistry.
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Affiliation(s)
- Jinjin Li
- Key Laboratory for
Thin Film and Microfabrication of Ministry of Education, Department
of Micro/Nano-electronics, Shanghai Jiao
Tong University, 800 Dong Chuan Road, Shanghai 200240, P. R. China
| | - Yuriy A. Abramov
- Pfizer
Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Michael F. Doherty
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106-5080, United States
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8
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Yakushev EY, Mikhaleva EA, Abramov YA, Sokolova OA, Zyrianova IM, Gvozdev VA, Klenov MS. [The role of Piwi nuclear localization in the differentiation and proliferation of germline stem cells]. Mol Biol (Mosk) 2016; 50:713-720. [PMID: 27668609 DOI: 10.7868/s0026898416040157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 02/09/2016] [Indexed: 11/23/2022]
Abstract
The Piwi protein and its orthologs are considered as the key components of the piRNA machinery implicated in transcriptional silencing of transposons. Неre, we show that nuclear localization of the Piwi protein is required not only for transposon repression, but also for proper differentiation of germline stem cells (GSCs). piwi^(Nt) mutation that causes loss of nuclear Piwi and its retention in the cytoplasm leads to the accumulation of undifferentiated GSC-like cells. The analysis of piwi^(Nt) mutation in combination with a bam gene mutation blocking GSC differentiation shows that the loss of nuclear Piwi decreases GSC proliferation rate. This is accompanied by the accumulation of DNA double-strand breaks in GSCs that may be caused by transposition events. Here, for the first time a set of transposons repressed by Piwi in GSCs and surrounding niche cells has been identified. The present study together with our previous data show that nuclear and cytoplasmic Piwi can regulate different stages of the functioning of germinal cells: cytoplasmic Piwi is sufficient to maintain GSCs, while nuclear Piwi localization is necessary for their proper proliferation and differentiation.
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Affiliation(s)
- E Y Yakushev
- Institute of Molecular Genetics of the Russian Academy of Sciences, Moscow, 123182 Russia
| | - E A Mikhaleva
- Institute of Molecular Genetics of the Russian Academy of Sciences, Moscow, 123182 Russia
| | - Y A Abramov
- Institute of Molecular Genetics of the Russian Academy of Sciences, Moscow, 123182 Russia
| | - O A Sokolova
- Institute of Molecular Genetics of the Russian Academy of Sciences, Moscow, 123182 Russia
| | - I M Zyrianova
- Institute of Molecular Genetics of the Russian Academy of Sciences, Moscow, 123182 Russia
| | - V A Gvozdev
- Institute of Molecular Genetics of the Russian Academy of Sciences, Moscow, 123182 Russia
| | - M S Klenov
- Institute of Molecular Genetics of the Russian Academy of Sciences, Moscow, 123182 Russia.,
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Abstract
Trans-inactivation is the repression of genes on a normal chromosome under the influence of a rearranged homologous chromosome demonstrating the position effect variegation (PEV). This phenomenon was studied in detail on the example of brownDominant allele causing the repression of wild-type brown gene on the opposite chromosome. We have investigated another trans-inactivation-inducing chromosome rearrangement, In(2)A4 inversion. In both cases, brownDominant and In(2)A4, the repression seems to be the result of dragging of the euchromatic region of the normal chromosome into the heterochromatic environment. It was found that cis-inactivation (classical PEV) and trans-inactivation show different patterns of distribution along the chromosome and respond differently to PEV modifying genes. It appears that the causative mechanism of trans-inactivation is de novo heterochromatin assembly on euchromatic sequences dragged into the heterochromatic nuclear compartment. Trans-inactivation turns out to be the result of a combination of heterochromatin-induced position effect and the somatic interphase chromosome pairing that is widespread in Diptera.
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Affiliation(s)
- Aleksei S Shatskikh
- a Department of Molecular Genetics of the Cell , Institute of Molecular Genetics, Russian Academy of Science , Moscow , Russia
| | - Yuriy A Abramov
- a Department of Molecular Genetics of the Cell , Institute of Molecular Genetics, Russian Academy of Science , Moscow , Russia
| | - Sergey A Lavrov
- a Department of Molecular Genetics of the Cell , Institute of Molecular Genetics, Russian Academy of Science , Moscow , Russia
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Caron G, Vallaro M, Ermondi G, Goetz GH, Abramov YA, Philippe L, Shalaeva M. A Fast Chromatographic Method for Estimating Lipophilicity and Ionization in Nonpolar Membrane-Like Environment. Mol Pharm 2016; 13:1100-10. [PMID: 26767433 DOI: 10.1021/acs.molpharmaceut.5b00910] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This study describes the design and implementation of a new chromatographic descriptor called log k'80 PLRP-S that provides information about the lipophilicity of drug molecules in the nonpolar environment, both in their neutral and ionized form. The log k'80 PLRP-S obtained on a polymeric column with acetonitrile/water mobile phase is shown to closely relate to log Ptoluene (toluene dielectric constant ε ∼ 2). The main intermolecular interactions governing log k'80 PLRP-S were deconvoluted using the Block Relevance (BR) analysis. The information provided by this descriptor was compared to ElogD and calclog Ptol, and the differences are highlighted. The "charge-flush" concept is introduced to describe the sensitivity of log k'80 PLRP-S to the ionization state of compounds in the pH range 2 to 12. The ability of log k'80 PLRP-S to indicate the propensity of neutral molecules and monoanions to form Intramolecular Hydrogen Bonds (IMHBs) is proven through a number of examples.
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Affiliation(s)
- Giulia Caron
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino , via Quarello 15, 10135 Torino, Italy
| | - Maura Vallaro
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino , via Quarello 15, 10135 Torino, Italy
| | - Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino , via Quarello 15, 10135 Torino, Italy
| | - Gilles H Goetz
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Yuriy A Abramov
- Worldwide Pharmaceutical Sciences, Pfizer Worldwide Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Laurence Philippe
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Marina Shalaeva
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
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Affiliation(s)
- Yuriy A. Abramov
- Pfizer Global Research and Development, Groton, Connecticut 06340, United States
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Docherty R, Pencheva K, Abramov YA. Low solubility in drug development: de-convoluting the relative importance of solvation and crystal packing. ACTA ACUST UNITED AC 2015; 67:847-56. [PMID: 25880016 DOI: 10.1111/jphp.12393] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 01/06/2015] [Indexed: 12/12/2022]
Abstract
OBJECTIVES An increasing trend towards low solubility is a major issue for drug development as formulation of low solubility compounds can be problematic. This paper presents a model which de-convolutes the solubility of pharmaceutical compounds into solvation and packing properties with the intention to understand the solubility limiting features. METHODS The Cambridge Crystallographic Database was the source of structural information. Lattice energies were calculated via force-field based approaches using Materials Studio. The solvation energies were calculated applying quantum chemistry models using Cosmotherm software. KEY FINDINGS The solubilities of 54 drug-like compounds were mapped onto a solvation energy/crystal packing grid. Four quadrants were identified were different balances of solvation and packing were defining the solubility. A version of the model was developed which allows for the calculation of the two features even in absence of crystal structure. CONCLUSION Although there are significant number of in-silico models, it has been proven very difficult to predict aqueous solubility accurately. Therefore, we have taken a different approach where the solubility is not predicted directly but is de-convoluted into two constituent features.
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Affiliation(s)
- Robert Docherty
- Pharmaceutical Sciences, Pfizer Global R&D, Sandwich, Kent, UK
| | | | - Yuriy A Abramov
- Pharmaceutical Sciences, Pfizer Global R&D, Sandwich, Kent, UK
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Chantigny YA, Murray JC, Kleinman EF, Robinson RP, Plotkin MA, Reese MR, Buckbinder L, McNiff PA, Millham ML, Schaefer JF, Abramov YA, Bordner J. 2-Aryl-3-methyloctahydrophenanthrene-2,3,7-triols as Potent Dissociated Glucocorticoid Receptor Agonists. J Med Chem 2015; 58:2658-77. [DOI: 10.1021/jm501601b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Yves A. Chantigny
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| | - John C. Murray
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Edward F. Kleinman
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ralph P. Robinson
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Michael A. Plotkin
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Matthew R. Reese
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Leonard Buckbinder
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Patricia A. McNiff
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Michele L. Millham
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jean F. Schaefer
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Yuriy A. Abramov
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jon Bordner
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, United States
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Abstract
The descriptors were determined, which can be most efficiently applied to virtual screening in order to provide answers to the following questions: 1) what is the propensity to form a solid state hydrate of a pharmaceutical compound, and 2) which coformer would provide for the highest stability with respect to relative humidity conditions?
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Sirin S, Kumar R, Martinez C, Karmilowicz MJ, Ghosh P, Abramov YA, Martin V, Sherman W. A computational approach to enzyme design: predicting ω-aminotransferase catalytic activity using docking and MM-GBSA scoring. J Chem Inf Model 2014; 54:2334-46. [PMID: 25005922 DOI: 10.1021/ci5002185] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Enzyme design is an important area of ongoing research with a broad range of applications in protein therapeutics, biocatalysis, bioengineering, and other biomedical areas; however, significant challenges exist in the design of enzymes to catalyze specific reactions of interest. Here, we develop a computational protocol using an approach that combines molecular dynamics, docking, and MM-GBSA scoring to predict the catalytic activity of enzyme variants. Our primary focuses are to understand the molecular basis of substrate recognition and binding in an S-stereoselective ω-aminotransferase (ω-AT), which naturally catalyzes the transamination of pyruvate into alanine, and to predict mutations that enhance the catalytic efficiency of the enzyme. The conversion of (R)-ethyl 5-methyl-3-oxooctanoate to (3S,5R)-ethyl 3-amino-5-methyloctanoate in the context of several ω-AT mutants was evaluated using the computational protocol developed in this work. We correctly identify the mutations that yield the greatest improvements in enzyme activity (20-60-fold improvement over wild type) and confirm that the computationally predicted structure of a highly active mutant reproduces key structural aspects of the variant, including side chain conformational changes, as determined by X-ray crystallography. Overall, the protocol developed here yields encouraging results and suggests that computational approaches can aid in the redesign of enzymes with improved catalytic efficiency.
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Affiliation(s)
- Sarah Sirin
- Schrödinger, Inc. , 120 West 45th Street, 29th Floor, New York, New York 10036, United States
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16
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Shalaeva M, Caron G, Abramov YA, O’Connell TN, Plummer MS, Yalamanchi G, Farley KA, Goetz GH, Philippe L, Shapiro MJ. Integrating Intramolecular Hydrogen Bonding (IMHB) Considerations in Drug Discovery Using ΔlogP As a Tool. J Med Chem 2013; 56:4870-9. [DOI: 10.1021/jm301850m] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marina Shalaeva
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Giulia Caron
- Molecular Biotechnology and
Health Sciences Department, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Yuriy A. Abramov
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Thomas N. O’Connell
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Mark S. Plummer
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Geeta Yalamanchi
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Kathleen A. Farley
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Gilles H. Goetz
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Laurence Philippe
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Michael J. Shapiro
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
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17
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Affiliation(s)
- Yuriy A. Abramov
- Pfizer Global Research and Development, Groton, Connecticut 06340, USA
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18
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Abramov YA, Loschen C, Klamt A. Rational coformer or solvent selection for pharmaceutical cocrystallization or desolvation. J Pharm Sci 2012; 101:3687-97. [PMID: 22821740 DOI: 10.1002/jps.23227] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 05/02/2012] [Accepted: 05/16/2012] [Indexed: 11/09/2022]
Abstract
It is demonstrated that the fluid-phase thermodynamics theory conductor-like screening model for real solvents (COSMO-RS) as implemented in the COSMOtherm software can be used for accurate and efficient screening of coformers for active pharmaceutical ingredient (API) cocrystallization. The excess enthalpy, H(ex) , between an API-coformer mixture relative to the pure components reflects the tendency of those two compounds to cocrystallize. Thus, predictive calculations may be performed with decent effort on a large set of molecular data in order to identify potentially new cocrystal systems. In addition, it is demonstrated that COSMO-RS theory allows reasonable ranking of coformers for API solubility improvement. As a result, experiments may be focused on those coformers, which have an increased probability of cocrystallization, leading to the largest improvement of the API solubility. In a similar way as potential coformers are identified for cocrystallization, solvents that do not tend to form solvates may be determined based on the highest H(ex) s with the API. The approach was successfully tested on tyrosine kinase inhibitor axitinib, which has a propensity to form relatively stable solvated structures with the majority of common solvents, as well as on thiophanate-methyl and thiophanate-ethyl benzimidazole fungicides, which form channel solvates.
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Affiliation(s)
- Yuriy A Abramov
- Pfizer Global Research and Development, Groton, Connecticut, USA.
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19
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Abramov YA. QTAIM Application in Drug Development: Prediction of Relative Stability of Drug Polymorphs from Experimental Crystal Structures. J Phys Chem A 2011; 115:12809-17. [DOI: 10.1021/jp2039515] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuriy A. Abramov
- Pfizer Global Research and Development, Groton, Conneticut, United States
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20
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Merzlikine A, Abramov YA, Kowsz SJ, Thomas VH, Mano T. Development of machine learning models of β-cyclodextrin and sulfobutylether-β-cyclodextrin complexation free energies. Int J Pharm 2011; 418:207-16. [PMID: 21497190 DOI: 10.1016/j.ijpharm.2011.03.065] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/16/2011] [Accepted: 03/24/2011] [Indexed: 12/13/2022]
Abstract
A new set of 142 experimentally determined complexation constants between sulfobutylether-β-cyclodextrin and diverse organic guest molecules, and 78 observations reported in literature, were used for the development of the QSPR models by the two machine learning regression methods - Cubist and Random Forest. Similar models were built for β-cyclodextrin using the 233-compound dataset available in the literature. These results demonstrate that the machine learning regression methods can successfully describe the complex formation between organic molecules and β-cyclodextrin or sulfobutylether-β-cyclodextrin. In particular, the root mean square errors for the test sets predictions by the best models are low, 1.9 and 2.7kJ/mol, respectively. The developed QSPR models can be used to predict the solubilizing effect of cyclodextrins and to help prioritizing experimental work in drug discovery.
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Affiliation(s)
- Alexei Merzlikine
- Department of Pharmaceutical Sciences, Pfizer Inc., Groton, CT, USA.
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21
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Campeta AM, Chekal BP, Abramov YA, Meenan PA, Henson MJ, Shi B, Singer RA, Horspool KR. Development of a targeted polymorph screening approach for a complex polymorphic and highly solvating API. J Pharm Sci 2010; 99:3874-86. [PMID: 20575000 DOI: 10.1002/jps.22230] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Elucidation of the most stable form of an active pharmaceutical ingredient (API) is a critical step in the development process. Polymorph screening for an API with a complex polymorphic profile can present a significant challenge. The presented case illustrates an extensively polymorphic compound with an additional propensity for forming stable solvates. In all, 5 anhydrous forms and 66 solvated forms have been discovered. After early polymorph screening using common techniques yielded mostly solvates and failed to uncover several key anhydrous forms, it became necessary to devise new approaches based on an advanced understanding of crystal structure and conformational relationships between forms. With the aid of this analysis, two screening approaches were devised which targeted high-temperature desolvation as a means to increase conformational populations and enhance overall probability of anhydrous form production. Application of these targeted approaches, comprising over 100 experiments, produced only the known anhydrous forms, without appearance of any new forms. The development of these screens was a critical and alternative approach to circumvent solvation issues associated with more conventional screening methods. The results provided confidence that the current development form was the most stable polymorph, with a low likelihood for the existence of a more-stable anhydrous form.
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Affiliation(s)
- Anthony M Campeta
- Pharmaceutical Sciences, Pfizer Global Research & Development, Groton, Connecticut 06340, USA.
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22
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Chekal BP, Campeta AM, Abramov YA, Feeder N, Glynn PP, McLaughlin RW, Meenan PA, Singer RA. The Challenges of Developing an API Crystallization Process for a Complex Polymorphic and Highly Solvating System. Part I. Org Process Res Dev 2009. [DOI: 10.1021/op9001559] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Brian P. Chekal
- Pfizer Global Research & Development, Pharmaceutical Sciences, Groton, Connecticut 06340, U.S.A., and Pfizer Global Research & Development, Pharmaceutical Sciences, Sandwich, U.K
| | - Anthony M. Campeta
- Pfizer Global Research & Development, Pharmaceutical Sciences, Groton, Connecticut 06340, U.S.A., and Pfizer Global Research & Development, Pharmaceutical Sciences, Sandwich, U.K
| | - Yuriy A. Abramov
- Pfizer Global Research & Development, Pharmaceutical Sciences, Groton, Connecticut 06340, U.S.A., and Pfizer Global Research & Development, Pharmaceutical Sciences, Sandwich, U.K
| | - Neil Feeder
- Pfizer Global Research & Development, Pharmaceutical Sciences, Groton, Connecticut 06340, U.S.A., and Pfizer Global Research & Development, Pharmaceutical Sciences, Sandwich, U.K
| | - Paul P. Glynn
- Pfizer Global Research & Development, Pharmaceutical Sciences, Groton, Connecticut 06340, U.S.A., and Pfizer Global Research & Development, Pharmaceutical Sciences, Sandwich, U.K
| | - Robert W. McLaughlin
- Pfizer Global Research & Development, Pharmaceutical Sciences, Groton, Connecticut 06340, U.S.A., and Pfizer Global Research & Development, Pharmaceutical Sciences, Sandwich, U.K
| | - Paul A. Meenan
- Pfizer Global Research & Development, Pharmaceutical Sciences, Groton, Connecticut 06340, U.S.A., and Pfizer Global Research & Development, Pharmaceutical Sciences, Sandwich, U.K
| | - Robert A. Singer
- Pfizer Global Research & Development, Pharmaceutical Sciences, Groton, Connecticut 06340, U.S.A., and Pfizer Global Research & Development, Pharmaceutical Sciences, Sandwich, U.K
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23
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Robinson RP, Buckbinder L, Haugeto AI, McNiff PA, Millham ML, Reese MR, Schaefer JF, Abramov YA, Bordner J, Chantigny YA, Kleinman EF, Laird ER, Morgan BP, Murray JC, Salter ED, Wessel MD, Yocum SA. Octahydrophenanthrene-2,7-diol Analogues as Dissociated Glucocorticoid Receptor Agonists: Discovery and Lead Exploration. J Med Chem 2009; 52:1731-43. [DOI: 10.1021/jm801512v] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ralph P. Robinson
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340
| | - Leonard Buckbinder
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340
| | - Amber I. Haugeto
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340
| | - Patricia A. McNiff
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340
| | - Michele L. Millham
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340
| | - Matthew R. Reese
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340
| | - Jean F. Schaefer
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340
| | - Yuriy A. Abramov
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340
| | - Jon Bordner
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340
| | - Yves A. Chantigny
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340
| | - Edward F. Kleinman
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340
| | - Ellen R. Laird
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340
| | - Bradley P. Morgan
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340
| | - John C. Murray
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340
| | - Eben D. Salter
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340
| | - Matthew D. Wessel
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340
| | - Sue A. Yocum
- Pfizer Global Research & Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340
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24
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McClure KF, Letavic MA, Kalgutkar AS, Gabel CA, Audoly L, Barberia JT, Braganza JF, Carter D, Carty TJ, Cortina SR, Dombroski MA, Donahue KM, Elliott NC, Gibbons CP, Jordan CK, Kuperman AV, Labasi JM, Laliberte RE, McCoy JM, Naiman BM, Nelson KL, Nguyen HT, Peese KM, Sweeney FJ, Taylor TJ, Trebino CE, Abramov YA, Laird ER, Volberg WA, Zhou J, Bach J, Lombardo F. Structure–activity relationships of triazolopyridine oxazole p38 inhibitors: Identification of candidates for clinical development. Bioorg Med Chem Lett 2006; 16:4339-44. [PMID: 16759861 DOI: 10.1016/j.bmcl.2006.05.056] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Revised: 05/15/2006] [Accepted: 05/16/2006] [Indexed: 12/21/2022]
Abstract
The synthesis, structure-activity relationship, in vivo activity, and metabolic profile for a series of triazolopyridine-oxazole based p38 inhibitors are described. The deficiencies of the lead structure in the series, CP-808844, were overcome by changes to the C4 aryl group and the triazole side-chain culminating in the identification of several potential clinical candidates.
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Affiliation(s)
- Kim F McClure
- Pfizer Global Research and Development, Groton Laboratories, CT 06340, USA.
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25
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McClure KF, Abramov YA, Laird ER, Barberia JT, Cai W, Carty TJ, Cortina SR, Danley DE, Dipesa AJ, Donahue KM, Dombroski MA, Elliott NC, Gabel CA, Han S, Hynes TR, Lemotte PK, Mansour MN, Marr ES, Letavic MA, Pandit J, Ripin DB, Sweeney FJ, Tan D, Tao Y. Theoretical and Experimental Design of Atypical Kinase Inhibitors: Application to p38 MAP Kinase. J Med Chem 2005; 48:5728-37. [PMID: 16134941 DOI: 10.1021/jm050346q] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mimics of the benzimidazolone nucleus found in inhibitors of p38 kinase are proposed, and their theoretical potential as bioisosteres is described. A set of calculated descriptors relevant to the anticipated binding interaction for the fragments 1-methyl-1H-benzotriazole 5, 3-methyl-benzo[d]isoxazole 3, and 3-methyl-[1,2,4]triazolo[4,3-a]pyridine 4, pyridine 1, and 1,3-dimethyl-1,3-dihydro-benzoimidazol-2-one 2 are reported. The design considerations and synthesis of p38 inhibitors based on these H-bond acceptor fragments is detailed. Comparative evaluation of the pyridine-, benzimidazolone-, benzotriazole-, and triazolopyridine-based inhibitors shows the triazoles 20 and 25 to be significantly more potent experimentally than the benzimidazolone after which they were modeled. An X-ray crystal structure of 25 bound to the active site shows that the triazole group serves as the H-bond acceptor but unexpectedly as a dual acceptor, inducing movement of the crossover connection of p38alpha. The computed descriptors for the hydrophobic and pi-pi interaction capacities were the most useful in ranking potency.
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Affiliation(s)
- Kim F McClure
- Pfizer Global Research and Development, Groton Laboratories, Eastern Point Road, Groton, Connecticut 06340, USA.
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26
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Li X, Wu G, Abramov YA, Volkov AV, Coppens P. Application of charge density methods to a protein model compound: calculation of Coulombic intermolecular interaction energies from the experimental charge density. Proc Natl Acad Sci U S A 2002; 99:12132-7. [PMID: 12221293 PMCID: PMC129410 DOI: 10.1073/pnas.192438999] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A combined experimental and theoretical charge density study of the pentapeptide Boc-Gln-d-Iva-Hyp-Ala-Phol (Boc, butoxycarbonyl; Gln, glutamine; Iva, isovaline; Hyp, hydroxyproline; Ala, ethylalanine; Phol, phenylalaninol) is described. The experimental analysis, based on synchrotron x-ray data collected at 20 K, is combined with ab initio theoretical calculations. The topologies of the experimental and theoretical densities are analyzed in terms of the atoms in molecules quantum theory. Topological parameters, including atomic charges and higher moments integrated over the atomic basins, have been evaluated with the program topxd and are used to calculate the electrostatic interactions between the molecules in the crystal. The interaction energies obtained after adding dispersive and repulsive van der Waals contributions agree quite well with those based on M-B3LYP/6-31G** dimer calculations for two of the three dimers in the crystal, whereas for the third a larger stabilization is obtained than predicted by the calculation. The agreement with theory is significantly better than that obtained with multipole moments derived directly from the aspherical atom refinement. The convergence of the interaction as a function of addition of successively higher moments up to and including hexadecapoles (l = 4) is found to be within 2-3 kJ/mol. Although shortcomings of both the theoretical and experimental procedures are pointed out, the agreement obtained supports the potential of the experimental method for the evaluation of interactions in larger biologically relevant molecules.
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Affiliation(s)
- Xue Li
- Chemistry Department, State University of New York, Buffalo, NY 14260-3000, USA
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27
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Volkov A, Abramov YA, Coppens P. Density-optimized radial exponents for X-ray charge-density refinement from ab initio crystal calculations. Acta Crystallogr A 2001; 57:272-82. [PMID: 11326112 DOI: 10.1107/s0108767300018547] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2000] [Accepted: 11/24/2000] [Indexed: 11/11/2022] Open
Abstract
Structure factors based on periodic density-functional (DFT) calculations on 25 molecular crystals have been used to evaluate trends in refined values of the kappa and kappa' expansion-contraction parameters of the Hansen-Coppens multipole formalism. As found previously and expected physically, the spherical-valence-shell kappa parameters are closely related to the net atomic charges, negative atoms being expanded and vice versa. kappa' parameters, which scale the radial dependence of the non-spherical deformation functions, are remarkably consistent for particular bonding environments. Systematic trends are observed for both carbon and oxygen, but the values obtained for nitrogen show a larger variation. Average values for oxygen and carbon in different bonding environments are tabulated and can be used whenever refinement of experimental data is affected by lack of uniqueness of the charge-density parameter set. Values for nitrogen must be more finely tuned to the specific bonding environment. The relation between atomic charge and kappa offers the possibility of introducing a constraint in the charge-density refinement of very large molecules, for which reduction of the size of the parameter set may be essential.
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Affiliation(s)
- A Volkov
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA
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28
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Abramov YA, Volkov A, Wu G, Coppens P. The experimental charge-density approach in the evaluation of intermolecular interactions. Application of a new module of the XD programming package to several solids including a pentapeptide. Acta Crystallogr A 2000; 56:585-91. [PMID: 11058845 DOI: 10.1107/s0108767300011405] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2000] [Accepted: 08/16/2000] [Indexed: 11/10/2022] Open
Abstract
A new module interfaced to the XD programming package has been used in the evaluation of intermolecular interactions and lattice energies of the crystals of p-nitroaniline, L-asparagine monohydrate and the pentapeptide Boc-Gln-D-Iva-Hyp-Ala-Phol (Boc = butoxycarbonyl, Iva = isovaline = ethylalanine, Phol = phenylalaninol). The electrostatic interactions are evaluated with the atom-centered distributed multipoles from KRMM (kappa'-restricted multipole model) refinements, using the Buckingham expression for non-overlapping charge densities. Results for p-nitroaniline are compared with Hartree-Fock (HF), density functional (DFT) and Moller-Plesset (MP2) supermolecular calculations and with HF and DFT periodic calculations. The HF and DFT methods fail to predict the stability of the p-nitroaniline crystal but the results of the experimental charge-density approach (ECDA) are in good agreement with both MP2 interaction energies and the experimental lattice energy. ECDA results for L-asparagine monohydrate compare well with those from DFT supermolecular and periodic HF calculations. The disorder of the terminal group in the pentapeptide, which persists at the experimental temperature of 20 K, corresponds to an energy difference of only 0.35 kJ mol(-1), which is too small to be reproduced with current methods.
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Affiliation(s)
- Y A Abramov
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 1460-3000, USA.
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29
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Abramov YA, Volkov A, Wu G, Coppens P. Use of X-ray Charge Densities in the Calculation of Intermolecular Interactions and Lattice Energies: Application to Glycylglycine, dl-Histidine, and dl-Proline and Comparison with Theory. J Phys Chem B 2000. [DOI: 10.1021/jp994319l] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuriy A. Abramov
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 1460-3000
| | - Anatoliy Volkov
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 1460-3000
| | - Guang Wu
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 1460-3000
| | - Philip Coppens
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, 1460-3000
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30
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Abramov YA, Brammer L, Klooster WT, Bullock RM. Experimental Charge Density and Neutron Structural Study of cis-HMn(CO)4PPh3: Comprehensive Analysis of Chemical Bonding and Evidence for a C−H···H−Mn Hydrogen Bond. Inorg Chem 1998. [DOI: 10.1021/ic9809660] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuriy A. Abramov
- Department of Chemistry, University of MissouriSt. Louis, 8001 Natural Bridge Road, St. Louis, Missouri 63121-4499, and Chemistry Department, Brookhaven National Laboratory, P.O. Box 5000, Upton, New York 11973-5000
| | - Lee Brammer
- Department of Chemistry, University of MissouriSt. Louis, 8001 Natural Bridge Road, St. Louis, Missouri 63121-4499, and Chemistry Department, Brookhaven National Laboratory, P.O. Box 5000, Upton, New York 11973-5000
| | - Wim T. Klooster
- Department of Chemistry, University of MissouriSt. Louis, 8001 Natural Bridge Road, St. Louis, Missouri 63121-4499, and Chemistry Department, Brookhaven National Laboratory, P.O. Box 5000, Upton, New York 11973-5000
| | - R. Morris Bullock
- Department of Chemistry, University of MissouriSt. Louis, 8001 Natural Bridge Road, St. Louis, Missouri 63121-4499, and Chemistry Department, Brookhaven National Laboratory, P.O. Box 5000, Upton, New York 11973-5000
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31
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Affiliation(s)
- Yuriy A. Abramov
- Department of Chemistry, University of MissouriSt. Louis, 8001 Natural Bridge Road, St. Louis, Missouri 63121-4499
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32
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Egorov YS, Abalmasov KG, Ivanov VV, Abramov YA, Gainulin RM, Chatterjee SS, Khussainov BE. Autotransplantation of the greater omentum in the treatment of chronic lymphedema. Lymphology 1994; 27:137-43. [PMID: 7807986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We evaluated the use of transplantation of the greater omentum in the management of chronic lymphedema in 21 patients. The omentum provides a large surface with fluid absorbing capability and potentially therefore is useful in management of patients with primary or hypoplastic peripheral lymphatics. Based on the angio- and lymphangio-architecture of the gastroepiploic architecture, we used large segments of greater omentum as a free autotransplant with microrevascularization to the femoral or axillary artery and vein thereby avoiding technical drawbacks of a pedicle graft with the feeding vessels traversing the abdomen. Elongation of the omentum must be done properly because omental lymphatic arcades do not consistently follow the blood vascular arcades in its more distal part. Accordingly, if not properly mobilized the blood supply may be retained whereas the lymph circulation is interrupted. We combined omental implantation with lymph nodal-venous anastomoses using an omental vein with a nearby systemic venous tributary. In 19 of the 21 patients followed from 3 months to 2 years after operation, remission of lymphedema was good (reduction in swelling more than 50%) in 14 patients and satisfactory in 5 (approximately 25-50% reduction in swelling) with improvement gradually increasing with the passage of time.
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Affiliation(s)
- Y S Egorov
- Department of Plastic and Reconstructive Microsurgery, Central Institute for Advanced Medical Studies, Moscow, Commonwealth of Independent States
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Abalmasov KG, Egorov YS, Abramov YA, Chatterjee SS, Uvarov DL, Neiman VA. Evaluation of the greater omentum in the treatment of experimental lymphedema. Lymphology 1994; 27:129-36. [PMID: 7807985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Despite advances in microsurgery, the most suitable operation for primary lymphedema remains unclear. A variety of tissue transplants and artificial substances have been used to facilitate drainage of peripheral lymph. The greater omentum, for example, has absorptive lymph draining capability, fights infection, and is expendable for the abdomen. Previous attempts to use the omentum in treatment of clinical lymphedema have, however, been disappointing. This discrepancy between theory and outcome prompted us to reevaluate the role of the omentum in the treatment of chronic lymphedema. In rabbits, mobilization of omentum was carefully examined by three separate techniques and the presence of natural lymph nodal-venous (L-V) shunts determined by an injection of Evans blue into the omentum with sampling later of plasma from the gastroepiploic venous blood. In dogs after promotion of unilateral chronic hindlimb lymphedema by soft tissue excision and sclerosis, the results of four methods of omental transplantation with or without L-V shunt for relief of lymphedema were compared. The results in rabbits suggest that although the greater omentum can be lengthened without jeopardizing its blood supply, it is inappropriate to lengthen it based on blood vascular arcades alone because the omental lymphatics do not strictly follow these arcades in the more distal portion, and with elongation, may be interrupted even though the blood supply remains intact. Moreover, because there is no natural L-V shunt within the greater omentum, the addition of a L-V shunt in dogs in addition to omental transplantation seems to increase effectiveness of the omentum for draining hindlimb lymph after its autotransplantation.
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Affiliation(s)
- K G Abalmasov
- Department of Plastic and Reconstructive Microsurgery, Central Institute for Advanced Medical Sciences, Moscow, Commonwealth of Independent States
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Abalmasov KG, Abramov YA, Egorov YS, Chatterjee SS. Enteromesenteric bridge in the treatment o primary lymphedema--a case report. Indian J Med Sci 1993; 47:131-135. [PMID: 8225456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Technical details and associated problems of enteromesenteric bridging operation for primary lymphedema (proximal obstructive hypoplasia) are discussed. The short term results are encouraging.
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Affiliation(s)
- K G Abalmasov
- Dept. of Plastic & Reconstructive Microsurgery, Central Institute for Advanced Medical Studies, Moscow, USSR
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