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Nishio M, Umezawa Y, Fantini J, Weiss MS, Chakrabarti P. CH-π hydrogen bonds in biological macromolecules. Phys Chem Chem Phys 2015; 16:12648-83. [PMID: 24836323 DOI: 10.1039/c4cp00099d] [Citation(s) in RCA: 335] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.
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Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338, Minamioya, Machida-shi, Tokyo 194-0031, Japan.
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2
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Modeling the molecular basis for α4β1 integrin antagonism. Bioorg Med Chem 2011; 19:5903-11. [PMID: 21889349 DOI: 10.1016/j.bmc.2011.08.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 07/29/2011] [Accepted: 08/05/2011] [Indexed: 11/23/2022]
Abstract
We report a 3D QSAR study of almost 300 structurally diverse small molecule antagonists of the integrin α4β1 whose biological activity spans six orders of magnitude. The alignment of the molecules was based on the conformation of a structurally related ligand bound to the αIIBβ3 and αvβ3 integrins in X-ray crystallographic studies. The molecular field method, CoMSIA, was used to generate the 3D QSAR models. The resulting models showed that the lipophilic properties were the most important, with hydrogen bond donor and steric properties less relevant. The models were highly significant (r(2)=0.89, q2(LOO)=0.67, r(2) (test set)=0.76), and could make robust predictions of the data (SEE=0.46, SEP=0.78, SEP (test set)=0.66). We predicted the antagonist activities of a further ten compounds with useful accuracy. The model appears capable of predicting α4β1 integrin antagonist activity to within a factor of five for compounds within its domain of applicability. The implications for design of improved integrin antagonists will be discussed.
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Takahashi O, Kohno Y, Nishio M. Relevance of weak hydrogen bonds in the conformation of organic compounds and bioconjugates: evidence from recent experimental data and high-level ab initio MO calculations. Chem Rev 2011; 110:6049-76. [PMID: 20550180 DOI: 10.1021/cr100072x] [Citation(s) in RCA: 447] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osamu Takahashi
- Department of Chemistry, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan.
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4
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Nishio M, Umezawa Y, Honda K, Tsuboyama S, Suezawa H. CH/π hydrogen bonds in organic and organometallic chemistry. CrystEngComm 2009. [DOI: 10.1039/b902318f] [Citation(s) in RCA: 481] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Lassoie MA, Broeders F, Collart P, Defrère L, de Laveleye-Defais F, Demaude T, Gassama A, Guillaumet G, Hayez JC, Kiss L, Knerr L, Nicolas JM, Norsikian S, Quéré L, Routier S, Verbois V, Provins L. 2,6-Quinolinyl derivatives as potent VLA-4 antagonists. Bioorg Med Chem Lett 2007; 17:142-6. [PMID: 17035017 DOI: 10.1016/j.bmcl.2006.09.069] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2006] [Revised: 09/22/2006] [Accepted: 09/23/2006] [Indexed: 10/24/2022]
Abstract
A new series of 2,6-quinolinyl derivatives was prepared leading to potent low nanomolar VLA-4/VCAM-1 antagonists.
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Okigami H, Takeshita K, Tajimi M, Komura H, Albers M, Lehmann TE, Rölle T, Bacon KB. Inhibition of eosinophilia in vivo by a small molecule inhibitor of very late antigen (VLA)-4. Eur J Pharmacol 2006; 559:202-9. [PMID: 17234179 DOI: 10.1016/j.ejphar.2006.11.065] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2006] [Revised: 11/21/2006] [Accepted: 11/30/2006] [Indexed: 12/17/2022]
Abstract
The alpha4beta1 integrin (very late antigen-4, VLA-4) plays an important role in the migration of lymphocytes, monocytes, and eosinophils, but not neutrophils, to sites of inflammation. Pharmacological antagonism of VLA-4 is an attractive prospect for the treatment of predominantly eosinophil mediated diseases such as asthma and allergic rhinitis. We report here on a potent and selective, small molecule VLA-4 inhibitor, (2S)-3-(2', 5'-dichlorobiphenyl-4-yl)-2-({[1-(2-methoxybenzoyl)piperidin-3-yl]carbonyl}amino) propanoic acid, compound 1, and characterize the antagonist activities of this molecule in various cell-based assays and in an animal model of eosinophil migration. Compound 1 inhibited VLA-4/ vascular cell adhesion molecule-1(VCAM-1) interactions with in vitro potencies (IC50 value of 210 nM) in VLA-4-expressing Ramos cells, although the compound did not inhibit cell adhesion to fibronectin via alpha5beta1 integrin (very late antigen-5, VLA-5). Blockade of phorbol-12-myristate-13-acetate (PMA)- or Mn2+-stimulated VLA-4 interactions with compound 1 was observed in human T lymphocytes (IC50 value of 230 nM), human eosinophils (IC50 value of 4.0 microM) and mouse eosinophils (IC50 value of 1.6 microM). Furthermore, compound 1 administered by intraperitoneal injection inhibited eosinophil infiltration in a dose-dependent manner by up to 80% in an air pouch model. These data support the use of small molecule VLA-4 antagonists in the treatment of relevant diseases, such as asthma, atopic dermatitis, or allergic rhinitis.
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Affiliation(s)
- Hiromi Okigami
- Bayer Yakuhin, Ltd., Research Center Kyoto, Respiratory Disease Research, Japan.
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Dyatkin AB, Gong Y, Miskowski TA, Kimball ES, Prouty SM, Fisher MC, Santulli RJ, Schneider CR, Wallace NH, Hornby PJ, Diamond C, Kinney WA, Maryanoff BE, Damiano BP, He W. Aza-bicyclic amino acid carboxamides as α4β1/α4β7 integrin receptor antagonists. Bioorg Med Chem 2005; 13:6693-702. [PMID: 16112583 DOI: 10.1016/j.bmc.2005.07.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2005] [Revised: 07/19/2005] [Accepted: 07/19/2005] [Indexed: 01/11/2023]
Abstract
A series of N-carboxy, N-alkyl, and N-carboxamido azabicyclo[2.2.2]octane carboxamides were prepared and assayed for inhibition of alpha4beta1-VCAM-1 and alpha4beta7-MAdCAM-1 interactions. Potency and alpha4beta1/alpha4beta7 selectivity were sensitive to the substituent R1-R3 in the structures 6, 7, and 8. Several compounds demonstrated low nanomolar balanced alpha4beta1/alpha4beta7 in vitro activity. Two compounds were selected for in vivo leukocytosis studies and demonstrated increases in circulating lymphocytes up to 250% over control.
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Affiliation(s)
- Alexey B Dyatkin
- Drug Discovery, Johnson & Johnson Pharmaceutical Research & Development, LLC., Spring House, PA 19477-0776, USA.
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Hoshina Y, Ikegami S, Okuyama A, Fukui H, Inoguchi K, Maruyama T, Fujimoto K, Matsumura Y, Aoyama A, Harada T, Tanaka H, Nakamura T. 2,3-Diphenylpropionic acids as potent VLA-4 antagonists. Bioorg Med Chem Lett 2005; 15:217-20. [PMID: 15582442 DOI: 10.1016/j.bmcl.2004.09.089] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Accepted: 09/30/2004] [Indexed: 10/26/2022]
Abstract
The discovery and SAR of 2,3-diphenylpropionic acid derivatives as highly potent VLA-4 antagonists are described. One representative compound, 9cc has inhibited intercellular adhesion by a VCAM-1/VLA-4 interaction with an IC(50) of 1.7 nM, and has good pharmacokinetics and oral bioavailability.
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Affiliation(s)
- Yoichiro Hoshina
- Central Research Laboratories, Kaken Pharmaceutical Co. Ltd, 14 Shinomiya-minamikawara, Yamashina, Kyoto 607-8042, Japan
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9
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Dyatkin AB, Hoekstra WJ, Kinney WA, Kontoyianni M, Santulli RJ, Kimball ES, Fisher MC, Carolyn Fisher M, Prouty SM, Abraham WM, de Garavilla L, Andrade-Gordon P, Hlasta DJ, He W, Hornby PJ, Damiano BP, Maryanoff BE. Aza-bicyclic amino acid sulfonamides as alpha(4)beta(1)/alpha(4)beta(7) integrin antagonists. Bioorg Med Chem Lett 2004; 14:591-6. [PMID: 14741249 DOI: 10.1016/j.bmcl.2003.11.063] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The design, synthesis, and biological activity of novel alpha(4)beta(1) and alpha(4)beta(7) integrin antagonists, containing a bridged azabicyclic nucleus, are reported. Conformational analysis of targets containing an azabicyclo[2.2.2]octane carboxylic acid and known integrin antagonists indicated that this azabicycle would be a suitable molecular scaffold. Variation of substituents on the pendant arylsulfonamide and phenylalanine groups resulted in potent alpha(4)beta(1)-selective and dual alpha(4)beta(1)/alpha(4)beta(7) antagonists. Potent compounds 11i, 11h, and 14 were effective in the antigen-sensitized sheep model of asthma.
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Affiliation(s)
- Alexey B Dyatkin
- Drug Discovery, Johnson & Johnson Pharmaceutical Research & Development, LLC, Spring House, PA 19477-0776, USA.
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10
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Huryn DM, Ashwell S, Baudy R, Dressen DB, Gallaway W, Grant FS, Konradi A, Ley RW, Petusky S, Pleiss MA, Sarantakis D, Semko CM, Sherman MM, Tio C, Zhang L. Synthesis, characterization and evaluation of pro-drugs of VLA-4 antagonists. Bioorg Med Chem Lett 2004; 14:1651-4. [PMID: 15026043 DOI: 10.1016/j.bmcl.2004.01.062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2003] [Accepted: 01/22/2004] [Indexed: 10/26/2022]
Abstract
A pro-drug strategy to identify orally efficacious VLA-4 antagonists is described. Potential pro-drugs were evaluated for their physical chemical characteristics and in vitro properties, including solubility, stability, permeability and plasma stability. Based on this characterization, promising compounds were identified for in vivo pharmacokinetic evaluation. These studies resulted in the identification of a pro-drug that exhibited desirable blood levels in PK studies in several different species.
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Affiliation(s)
- Donna M Huryn
- Chemical & Screening Sciences, Wyeth Research, CN 8000, Princeton, NJ 08543, USA.
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11
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Abstract
Many lead compounds with the potential to progress to viable drug candidates have been identified from libraries during the past two years. There are two key strategies most often employed to find leads from libraries: first, high-throughput biological screening of corporate compound collections; and second, synthesis and screening of project-directed libraries (i.e. target-based libraries). Numerous success stories, including the discovery of several clinical candidates, testify to the utility of chemical library collections as proven sources of new leads for drug development.
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Affiliation(s)
- Adam Golebiowski
- Procter & Gamble Pharmaceuticals, Health Care Research Center, Mason, OH 45040-8006, USA.
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Porter JR, Archibald SC, Brown JA, Childs K, Critchley D, Head JC, Parton TAH, Robinson MK, Shock A, Taylor RJ, Warrellow GJ. Dehydrophenylalanine derivatives as VLA-4 integrin antagonists. Bioorg Med Chem Lett 2003; 13:805-8. [PMID: 12617895 DOI: 10.1016/s0960-894x(03)00019-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We describe a series of dehydrophenylalanine derivatives where the Z isomers are potent VLA-4 antagonists but are subject to rapid biliary clearance and the E isomers have poor activity but have a slower rate of clearance. These configurationally constrained molecules have led to the design of a novel class of benzodiazepine VLA-4 antagonists.
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Affiliation(s)
- John R Porter
- Department of Medicinal Chemistry, Celltech R&D Ltd, 216 Bath Road, Slough SL1 4EN, UK.
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13
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Sidduri A, Tilley JW, Lou JP, Chen L, Kaplan G, Mennona F, Campbell R, Guthrie R, Huang TN, Rowan K, Schwinge V, Renzetti LM. N-Aroyl-L-phenylalanine derivatives as VCAM/VLA-4 antagonists. Bioorg Med Chem Lett 2002; 12:2479-82. [PMID: 12161162 DOI: 10.1016/s0960-894x(02)00387-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A series of N-benzoyl-4-[(2,6-dichlorobenzoyl)amino]-L-phenylalanine derivatives was prepared in order to optimize the substitution on the N-benzoyl moiety for VCAM/VLA-4 antagonist activity. Disubstitution in the 2- and 6-positions is favored and a range of small alkyl and halogen are tolerated. A model of the bioactive conformation of these compounds is proposed.
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