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Wu D, Zheng X, Liu R, Li Z, Jiang Z, Zhou Q, Huang Y, Wu XN, Zhang C, Huang YY, Luo HB. Free energy perturbation (FEP)-guided scaffold hopping. Acta Pharm Sin B 2022; 12:1351-1362. [PMID: 35530128 PMCID: PMC9072250 DOI: 10.1016/j.apsb.2021.09.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/03/2021] [Accepted: 09/24/2021] [Indexed: 12/01/2022] Open
Abstract
Scaffold hopping refers to computer-aided screening for active compounds with different structures against the same receptor to enrich privileged scaffolds, which is a topic of high interest in organic and medicinal chemistry. However, most approaches cannot efficiently predict the potency level of candidates after scaffold hopping. Herein, we identified potent PDE5 inhibitors with a novel scaffold via a free energy perturbation (FEP)-guided scaffold-hopping strategy, and FEP shows great advantages to precisely predict the theoretical binding potencies ΔG FEP between ligands and their target, which were more consistent with the experimental binding potencies ΔG EXP (the mean absolute deviations| Δ G FEP - Δ G EXP |  < 2 kcal/mol) than those ΔG MM-PBSA or ΔG MM-GBSA predicted by the MM-PBSA or MM-GBSA method. Lead L12 had an IC50 of 8.7 nmol/L and exhibited a different binding pattern in its crystal structure with PDE5 from the famous starting drug tadalafil. Our work provides the first report via the FEP-guided scaffold hopping strategy for potent inhibitor discovery with a novel scaffold, implying that it will have a variety of future applications in rational molecular design and drug discovery.
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Key Words
- ABFE, absolute binding free energy
- BAR, Bennet acceptance ratio
- Binding potencies
- DCM, dichloromethane
- DMF, N,N-dimethylformamide
- DMSO, dimethyl sulfoxide
- Drug discovery
- FEP, free energy perturbation
- Free energy perturbation
- GAFF, general AMBER force field
- HPLC, high performance liquid chromatography
- HRMS, High resolution mass spectra
- IC50, half-inhibitory concentration
- IPTG, isopropyl b-d-thiogalactopyranoside
- LV, left ventricle
- MAD, mean absolute deviations
- MD, molecular dynamics
- MM-GBSA, molecular mechanics/generalized born surface area
- Molecular design
- PAH, pulmonary arterial hypertension
- PDB, protein data bank
- PDE, phosphodiesterase
- PDE5 inhibitors
- PDE5, phosphodiesterase-5
- PME, particle mesh Ewald
- Privileged scaffolds
- Pulmonary arterial hypertension
- RBFE, relative binding free energy
- RED, restraint energy distribution
- RESP, restrained electrostatic potential
- RV, right ventricle
- RVHI, right ventricle hypertrophy index
- SARs, structure–activity relationships
- Scaffold hopping
- THF, tetrahydrofuran
- TLC, thin-layer chromatography
- WT, wall thickness
- ip, intraperitoneal injection
- iv, intravenous administration
- mPAP, pulmonary artery pressure
- po, oral administration (per os)
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Affiliation(s)
- Deyan Wu
- School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xuehua Zheng
- School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 511436, China
| | - Runduo Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhe Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zan Jiang
- School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 511436, China
| | - Qian Zhou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yue Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xu-Nian Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Chen Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yi-You Huang
- School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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Porwal K, Pal S, Bhagwati S, Siddiqi MI, Chattopadhyay N. Therapeutic potential of phosphodiesterase inhibitors in the treatment of osteoporosis: Scopes for therapeutic repurposing and discovery of new oral osteoanabolic drugs. Eur J Pharmacol 2021; 899:174015. [PMID: 33711307 DOI: 10.1016/j.ejphar.2021.174015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/19/2021] [Accepted: 03/03/2021] [Indexed: 01/05/2023]
Abstract
Cyclic nucleotide phosphodiesterases (PDEs) are ubiquitously expressed enzymes that hydrolyze phosphodiester bond in the second messenger molecules including cAMP and cGMP. A wide range of drugs blocks one or more PDEs thereby preventing the inactivation of cAMP/cGMP. PDEs are differentially expressed in bone cells including osteoblasts, osteoclasts and chondrocytes. Intracellular increases in cAMP/cGMP levels in osteoblasts result in osteogenic response. Acting via the type 1 PTH receptor, teriparatide and abaloparatide increase intracellular cAMP and induce osteoanabolic effect, and many PDE inhibitors mimic this effect in preclinical studies. Since all osteoanabolic drugs are injectable and that oral drugs are considered to improve the treatment adherence and persistence, osteogenic PDE inhibitors could be a promising alternative to the currently available osteogenic therapies and directly assessed clinically in drug repurposing mode. Similar to teriparatide/abaloparatide, PDE inhibitors while stimulating osteoblast function also promote osteoclast function through stimulation of receptor activator of nuclear factor kappa-B ligand production from osteoblasts. In this review, we critically discussed the effects of PDE inhibitors in bone cells from cellular signalling to a variety of preclinical models that evaluated the bone formation mechanisms. We identified pentoxifylline (a non-selective PDE inhibitor) and rolipram (a PDE4 selective inhibitor) being the most studied inhibitors with osteogenic effect in preclinical models of bone loss at ≤ human equivalent doses, which suggest their potential for post-menopausal osteoporosis treatment through therapeutic repurposing. Subsequently, we treated pentoxifylline and rolipram as prototypical osteogenic PDEs to predict new chemotypes via the computer-aided design strategies for new drugs, based on the structural biology of PDEs.
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Affiliation(s)
- Konica Porwal
- Division of Endocrinology and Centre for Research in Anabolic Skeletal Targets in Health and Illness (ASTHI), India
| | - Subhashis Pal
- Division of Endocrinology and Centre for Research in Anabolic Skeletal Targets in Health and Illness (ASTHI), India
| | - Sudha Bhagwati
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Sector 10/1 Jankipuram Extension, Sitapur Road, Lucknow, 226 031, India
| | - Mohd Imran Siddiqi
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Sector 10/1 Jankipuram Extension, Sitapur Road, Lucknow, 226 031, India
| | - Naibedya Chattopadhyay
- Division of Endocrinology and Centre for Research in Anabolic Skeletal Targets in Health and Illness (ASTHI), India.
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Jiang Z, Zheng X, Li Z, Pan S, Wang X, Zhang C, Li Z, Luo HB, Wu D, Cai X. 3D-QSAR modeling of Phosphodiesterase-5 inhibitors: evaluation and comparison of the receptor- and ligand-based alignments. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02311-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Teymouri Rad R, Dadashzadeh S, Vatanara A, Alavi S, Ghasemian E, Mortazavi SA. Tadalafil nanocomposites as a dry powder formulation for inhalation, a new strategy for pulmonary arterial hypertension treatment. Eur J Pharm Sci 2019; 133:275-286. [DOI: 10.1016/j.ejps.2019.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 03/09/2019] [Accepted: 04/01/2019] [Indexed: 10/27/2022]
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Wu D, Zhang T, Chen Y, Huang Y, Geng H, Yu Y, Zhang C, Lai Z, Wu Y, Guo X, Chen J, Luo HB. Discovery and Optimization of Chromeno[2,3-c]pyrrol-9(2H)-ones as Novel Selective and Orally Bioavailable Phosphodiesterase 5 Inhibitors for the Treatment of Pulmonary Arterial Hypertension. J Med Chem 2017; 60:6622-6637. [DOI: 10.1021/acs.jmedchem.7b00523] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Deyan Wu
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Tianhua Zhang
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Yiping Chen
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Yadan Huang
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Haiju Geng
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Yanfa Yu
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Chen Zhang
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Zengwei Lai
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Yinuo Wu
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Xiaolei Guo
- Infinitus (China) Co. Ltd., Guangzhou 510663, China
| | - Jianwen Chen
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Hai-Bin Luo
- School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
- Collaborative
Innovation Center of High Performance Computing, National University of Defense Technology, Changsha 410073, China
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Sen S, Thomas A, Das S, Dey JK, Peedicayil A, Thomas V, Peedicayil J. Inhibition by tadalafil of contractility of isolated nonpregnant human myometrium. J Pharmacol Pharmacother 2017; 7:177-181. [PMID: 28163539 PMCID: PMC5242031 DOI: 10.4103/0976-500x.195902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Objective: To investigate the inhibitory effect of tadalafil on the contractility of isolated nonpregnant human myometrium. Materials and Methods: The ability of tadalafil (25, 40, and 63 μM) to inhibit 55 mM KCl-induced contractility of isolated nonpregnant human myometrium was studied. The ability of the ATP-sensitive potassium channel blocker glibenclamide (10 μM) and the calcium-sensitive potassium channel (BKCa) blocker iberiotoxin (100 nM) to reverse the inhibitory effect of 40 μM tadalafil on 55 mM KCl-induced myometrial contractility was also studied. Results: Tadalafil produced a concentration-dependent inhibition of myometrial contractility that was statistically significant at 40 and 63 μM concentrations of tadalafil. The inhibition by tadalafil of myometrial contractility was statistically significantly reversed by the concurrent administration of glibenclamide and iberiotoxin. Conclusions: These results suggest that tadalafil inhibits human myometrial contractility by opening ATP-sensitive potassium channels and BKCa channels. The opening of these channels could have been due to the action of raised intracellular levels of cGMP due to inhibition of PDE-5 by tadalafil. The results suggest that tadalafil could be investigated for use in clinical conditions requiring relaxation of the myometrium.
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Affiliation(s)
- Sumalya Sen
- Department of Pharmacology and Clinical Pharmacology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Anitha Thomas
- Division of Obstetrics and Gynaecology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Saibal Das
- Department of Pharmacology and Clinical Pharmacology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Jayanta Kumar Dey
- Department of Pharmacology and Clinical Pharmacology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Abraham Peedicayil
- Division of Obstetrics and Gynaecology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Vinotha Thomas
- Division of Obstetrics and Gynaecology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Jacob Peedicayil
- Department of Pharmacology and Clinical Pharmacology, Christian Medical College, Vellore, Tamil Nadu, India
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Hahn SS, Makaryus M, Talwar A, Narasimhan M, Zaidi G. A review of therapeutic agents for the management of pulmonary arterial hypertension. Ther Adv Respir Dis 2016; 11:46-63. [PMID: 27595643 PMCID: PMC5941973 DOI: 10.1177/1753465816665289] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is an uncommon, progressive and life
threatening disease characterized by a proliferative vasculopathy of the small
muscular pulmonary arterioles resulting in elevated pulmonary vascular
resistance and eventually right ventricular failure. An increasing understanding
of the pathobiology of PAH and its natural history has led to the development of
numerous targeted therapies. Despite these advances there is significant
progression of disease and the survival rate remains low. This article reviews
the agents currently available for the medical management of PAH.
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Affiliation(s)
- Stella S Hahn
- Northwell Health Division of Pulmonary Critical Care and Sleep Medicine, 410 Lakeville Road, Suite 107, New Hyde Park, NY 11042, USA
| | - Mina Makaryus
- Northwell Health Division of Pulmonary Critical Care and Sleep Medicine, 410 Lakeville Road, Suite 107, New Hyde Park, NY 11042, USA
| | - Arunabh Talwar
- Northwell Health Division of Pulmonary Critical Care and Sleep Medicine, 410 Lakeville Road, Suite 107, New Hyde Park, NY 11042, USA
| | - Mangala Narasimhan
- Northwell Health Division of Pulmonary Critical Care and Sleep Medicine, 410 Lakeville Road, Suite 107, New Hyde Park, NY 11042, USA
| | - Gulrukh Zaidi
- Northwell Health Division of Pulmonary Critical Care and Sleep Medicine, 410 Lakeville Road, Suite 107, New Hyde Park, NY 11042, USA
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Gu S, Hu H, Dong H. Systematic Review of Health-Related Quality of Life in Patients with Pulmonary Arterial Hypertension. PHARMACOECONOMICS 2016; 34:751-770. [PMID: 26951248 DOI: 10.1007/s40273-016-0395-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
BACKGROUND The increasing survival of patients with pulmonary arterial hypertension (PAH) has shifted attention towards the disease burden that PAH imposes on patients and healthcare systems. Most studies emphasize epidemiology and medications, while large observational studies reporting on the health-related quality of life (HRQOL) of patients with PAH are lacking. OBJECTIVE Our objective was to study the HRQOL of patients with PAH and to summarize the factors that influence it. METHODS We conducted systematic literature searches in English (PubMed, Web of Knowledge, ScienceDirect and OVID) and Chinese (China National Knowledge Infrastructure, Wanfang Data, Chongqing VIP and SinoMed) databases to identify studies published from 2000 to 2015 assessing the HRQOL of patients with PAH. Search results were independently reviewed and extracted by two reviewers. RESULTS Of 3392 records identified in the initial search, 20 eligible papers (19 English, 1 Chinese) were finally included. Studies used a range of instruments; the generic 36-item Short Form Survey (SF-36) was the most widely used, and the disease-specific Cambridge Pulmonary Hypertension Outcome Survey (CAMPHOR) was the second mostly widely used. Mean HRQOL scores assessed via the SF-36 (physical component summary [PCS] 25.4-80.1; mental component summary [MCS] 33.2-76.0) and CAMPHOR (symptom scores 3.1-17; total HRQOL 2.8-12.6; activity scores 3.8-18.1) varied across studies, reporting decreased HRQOL in patients. Mental health (depression, anxiety, stress), physical health (exercise capacity, symptoms) and medical therapies were reported to affect HRQOL. CONCLUSION We found that PAH places a substantial burden on patients, particularly in terms of HRQOL; however, the paucity of large observational studies in this area requires the attention of researchers, especially in China.
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Affiliation(s)
- Shuyan Gu
- Center for Health Policy Studies, School of Public Health, Zhejiang University School of Medicine, 866 Yuhangtang Road, Hangzhou, Zhejiang Province, 310058, China
| | - Huimei Hu
- Center for Health Policy Studies, School of Public Health, Zhejiang University School of Medicine, 866 Yuhangtang Road, Hangzhou, Zhejiang Province, 310058, China
- Department of Public Health, Zhejiang Medical College, Hangzhou, Zhejiang Province, China
| | - Hengjin Dong
- Center for Health Policy Studies, School of Public Health, Zhejiang University School of Medicine, 866 Yuhangtang Road, Hangzhou, Zhejiang Province, 310058, China.
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Inhibition of phosphodiesterase 5 reduces bone mass by suppression of canonical Wnt signaling. Cell Death Dis 2014; 5:e1544. [PMID: 25429621 PMCID: PMC4260761 DOI: 10.1038/cddis.2014.510] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 01/21/2023]
Abstract
Inhibitors of phosphodiesterase 5 (PDE5) are widely used to treat erectile
dysfunction and pulmonary hypertension in clinics. PDE5, cyclic guanosine
monophosphate (cGMP), and protein kinase G (PKG) are important components of the
non-canonical Wnt signaling. This study aimed to investigate the effect of PDE5
inhibition on canonical Wnt signaling and osteoblastogenesis, using both in
vitro cell culture and in vivo animal models. In the in
vitro experiments, PDE5 inhibition resulted in activation of cGMP-dependent
protein kinase 2 and consequent inhibition of glycogen synthase kinase
3β phosphorylation, destabilization of cytosolic
β-catenin and the ultimate suppression of canonical Wnt signaling and
reduced osteoblastic differentiation in HEK293T and C3H10T1/2 cells. In animal
experiments, systemic inhibition of PDE5 suppressed the activity of canonical Wnt
signaling and osteoblastogenesis in bone marrow-derived stromal cells, resulting in
the reduction of bone mass in wild-type adult C57B/6 mice, significantly
attenuated secreted Frizzled-related protein-1 (SFRP1) deletion-induced activation of
canonical Wnt signaling and excessive bone growth in adult
SFRP1−/− mice. Together, these results uncover a
hitherto uncharacterized role of PDE5/cGMP/PKG signaling in bone homeostasis
and provide the evidence that long-term treatment with PDE5 inhibitors at a high
dosage may potentially cause bone catabolism.
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Norman P. Pulmonary arterial hypertension: a rare disease that encourages the development of multiple treatments. Expert Opin Orphan Drugs 2014. [DOI: 10.1517/21678707.2014.924851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Discovery of 3-(4-hydroxybenzyl)-1-(thiophen-2-yl)chromeno[2,3-c]pyrrol-9(2H)-one as a phosphodiesterase-5 inhibitor and its complex crystal structure. Biochem Pharmacol 2014; 89:86-98. [DOI: 10.1016/j.bcp.2014.02.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/12/2014] [Accepted: 02/14/2014] [Indexed: 12/25/2022]
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Oral therapies for pulmonary arterial hypertension: endothelin receptor antagonists and phosphodiesterase-5 inhibitors. Clin Chest Med 2014; 34:811-24. [PMID: 24267306 DOI: 10.1016/j.ccm.2013.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of orally active pulmonary vasodilators has been a major breakthrough in the treatment of pulmonary arterial hypertension (PAH). Orally active medications greatly enhanced patient access to PAH treatment and increased an interest in the diagnosis and treatment of this disease that still continues. Four different orally active drugs are currently available for the treatment of PAH and several more are undergoing evaluation. This article discusses the mechanisms by which endothelin receptor antagonists and phosphodiesterase-5 inhibitors mitigate pulmonary hypertensive responses, and reviews the most recent data concerning their efficacy and limitations in the treatment of PAH.
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