Computer-Aided Multitarget Drug Design and Inhibition Mechanism Studies of Human Chymase via Systems Biology, Molecular Modeling and QM Approaches

아루마렌 경상대학교 대학원 2013 국내박사

Chymase (EC 3.4.21.39) is an enzyme of the hydrolase class that catalyzes the hydrolysis of peptide bonds and it is abundant in secretory granules of mast cells. Chymase is the major extravascular source of vasoactive angiotensin II (Ang II). The octapeptide hormone, Ang II targets human heart and plays an important role in vascular proliferation, hypertension and atherosclerosis. Chymase also converts precursors of transforming growth factor-β (TGF-β) and matrix metalloproteinase (MMP)-9 to their active forms thus contributing to vascular response to injury. The multiple functions of chymase may play an important role in the development and promotion of various diseases. Therefore, chymase has become an emerging drug target for many diseases such as cardiovascular diseases, allergic inflammation, and fibrotic disorders. The main aim of this research work is to provide a new idea of multi-target drug design thus finding novel uses for human chymase inhibitors as well as to explore the inhibition mechanism of human chymase. Moreover, various computational approaches have been applied to find potential chymase inhibitors from various databases. In the first part, a robust computational strategy is developed that is applicable to any enzyme system and that allows the prediction of drug effects on biological processes. Putative off-targets for chymase inhibitors were identified through various structural and functional similarity analyses along with molecular docking studies. Finally, literature survey was carried out to incorporate these off-targets into various biological pathways and to establish links between pathways and particular adverse effects. Off-targets of chymase inhibitors are linked to various biological pathways such as classical and lectin pathways of complement system, intrinsic and extrinsic pathways of coagulation cascade, and fibrinolytic system. These off-targets and their associated pathways are elucidated for the affects of inflammation, cancer, hemorrhage, thrombosis and central nervous system diseases(Alzheimer’s disease). Prospectively, our approach is helpful not only to better understand the mechanisms of chymase inhibitors but also for drug repurposing exercises to find novel uses for these inhibitors. Moreover, this computational approach is also valuable for applications such as multitarget drug design and drug combinations. In the next part, to find novel and potent potential chymase inhibitors, various computational approaches such as structure and ligand-based pharmacophore modeling, molecular docking, database screening, and quantum mechanical (QM) techniques were applied. Finally, 11 compounds were selected as potential chymase inhibitors based on their strong binding affinity at the active site of chymase and key interactions with important active site residues. This study also illustrated that how multiple pharmacophore approach could be more useful in identifying structurally diverse hits which may bind to all possible bioactive conformations available in the active site of enzyme. In the third part of this work, binding mode of substrate (angiotensin I) was predicted for chymase and it was further applied in chymase inhibitor design. The binding orientation of three chymase inhibitors with very similar chemical structures but highly different inhibitory profile towards hydrolase function of chymase were also analyzed aiming at elucidating the origin for disparities in their biological activities. Result elucidates about the 3D chymase structural details as well as the importance of K40 in hydrolase function. Chymase complexes with the most active compound and substrate were used for development of a hybrid pharmacophore model which was applied in databases screening to find potential chymase inhibitors. In the final part, a computational investigation involving 2D/3D QSAR modeling techniques such as Bayesian and Genetic Function Approximation (GFA) modeling along with molecular docking and quantum chemical methodologies is performed on chymase and its novel 1,4-diazepane-2,5-diones inhibitors which explores the crucial molecular features contributing to binding specificity. This work is helpful to understand the relationships between molecular structures of inhibitors and their biological activities. This study is also useful to gain an insight into the binding mechanism between human chymase enzyme and its inhibitors. In conclusion, various computational strategies were developed involving human chymase enzyme and its inhibitors: (i) Multitarget drug design strategy was developed to find off-targets, biological pathways, and target diseases for chymase inhibitors. (ii) Multiple pharmacophore-based scheme was designed to identify potential chymase inhibitors. (iii)The binding mechanism between human chymase enzyme and its inhibitors was explored.(iv) Binding mode of substrate (angiotensin I) was predicted for chymase. On the whole, the computational strategies developed in this research exertion may not only be helpful in drug design of human chymase but may be generally applicable to design drugs for other enzymes as well.

Intramolecular Interactions in Pd(II) Complexes with Various Substituents : A Theoretical Study

아루마렌 경상대학교 대학원 2010 국내석사

In conclusion, this theoretical study reveals various trends in X…X distances in Pd(Ⅱ) complexes upon the variation in terminal ligands. This clearly signifies the major influence of the nature of terminal ligands on the strength of van der Waals X…X interactions. Moreover, a strong correlation between the X…X interactions and charge on X atoms of bridging ligand is also revealed. The A type complexes have exhibited minimum X…X distance in all furan, thiophene, and selenophene bridging oligomers containing complexes. Consequently, it could be concluded that substitution of uncharged terminal ligand may be more helpful to instigate short heteroatom-heteroatom interactions in this motif of Pd(Ⅱ) complexes than charged & uncharged, and charged terminal ligand containing complexes. Moreover, it was also revealed that number of short interactions among heteroatoms in selenophene containing Pd(Ⅱ) complexes were more than those in thiophene and furan containing complexes. While, Pd(Ⅱ) complexes with furan as bridging ligand showed less interactions between heteroatoms than thiophene. This, trend of X…X interactions could be related to the electron-retaining ability of heteroatoms. As the tendency of heteroatom to retain its electron increases, stability of heteroatom…heteroatom interactions decreases. Therefore, furan having most electronegative heteroatom showed weakest interactions and selenophene exhibited the strongest interactions. Thus, another important finding of this research work is that X…X interactions become stronger on going from O to Se. Consequently, in order to instigate short X…X interactions, choice of the appropriate bridging ligand is also an important factor along with the terminal ligands. Therefore, on the basis of these findings, it could be suggested that Pd(Ⅱ) complexes substituted with neutral terminal ligands and having selenophene oligomer as bridging oligomer could be used to activate short X…X interactions in this motif of Pd(Ⅱ) complexes. 헤테로고리 리간드를 가지는 Pd(Ⅱ) 전이금속 화합물들은 컨쥬게이트 리간드에 의해 전기적 및 광학적 성질이 발현되어, 지금까지 매력적인 연구대상으로 각광 받아왔다. 본 연구에서는 헤테로고리 화합물인 furan, thiophene, selenophene들이 가교 리간드 형태로 결합된 가교형 Pd(Ⅱ) 화합물에 연구의 초점을 두었다. Pd(Ⅱ) 화합물에 다양한 형태의 말단 리간드를 도입하여 계산하였으며, 또한 두 가교 리간드의 헤테로 원자들 사이의 상호 작용(O…O, S…S, Se…Se)에 의한 구조적 변화를 조사하였다. Pd는 LANL2DZ, 다른 원자는 3-21g*, 6-31g*의 기저함수를 사용하였으며, 계산 방법은 밀도범함수 이론 (DFT)를 사용하여 최적화하였다. 원자들의 전하는 NBO 방법을 사용하여 원자들의 전하 분포를 조사하였다. Pd(Ⅱ) 화합물의 경우, 말단 리간드의 종류에 따른 1) 양쪽에 전하가 없는 말단 리간드를 갖는 A 화합물, 2) 전하가 있는 것과 전하가 없는 말단 리간드를 갖는 B 화합물, 3) 양쪽 모두 전하가 있는 말단 리간드를 갖는 C 화합물들로 분류하였다. 또한, 중심 금속에서 말단 리간드의 환경 변화에 따른 영향과 Pd(Ⅱ) 화합물에서의 가교 리간드의 기하학적 구조를 자세히 조사하였다. 이러한 연구 결과, 중성 말단 리간드를 갖는 A 화합물들은 다른 화합물들에 비해 가교 리간드의 헤테로 원자 사이에 강한 상호 작용을 나타내었다. selenophene를 갖는 Pd(Ⅱ) 화합물이 thiophene, furan를 갖는 화합물보다 분자내 상호작용을 더 잘하는 것으로 밝혀졌다.