Investigation of binding characteristics of ritonavir with calf thymus DNA with the help of spectroscopic techniques and molecular simulation
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
Authors: Kou, Song-Bo; Zhou, Kai-Li; Lin, Zhen-Yi; Lou, Yan-Yue; Wang, Bao-Li; Shi, Jie-Hua; Liu, Ying-Xin
Abstract
The binding behavior of ritonavir (RTV), a HIV/AIDS protease inhibitor, with ct-DNA was characterized through multiple testing technologies and theoretical calculation. The findings revealed that the RTV-DNA complex was formed through the noncovalent interaction mainly including conventional hydrogen bonds and carbon hydrogen bonds as well as hydrophobic interactions (pi-alkyl interactions). The stoichiometry and binding constant of the RTV-DNA complex were 1:1 and 1.87 x 10(3) M-1 at 298 K, respectively, indicating that RTV has moderate affinity with ct-DNA. The findings confirmed that RTV binds to the minor groove of DNA. The outcomes of CD experiments showed that the binding with RTV changed the conformation of DNA slightly. However, the conformation of RTV had obvious changes after binding to DNA, meaning that the flexibility of RTV molecule played an important role in stabilizing the RTV-DNA complex. Meanwhile, the results of DFT calculation revealed that the RTV and DNA interaction caused the changes in the frontier molecular orbitals, dipole moment and atomic charge distribution of RTV, altering the chemical properties of RTV when it bound to DNA. Communicated by Ramaswamy H. Sarma
Connective Steiner 3-eccentricity index and network similarity measure
APPLIED MATHEMATICS AND COMPUTATION
Authors: Yu, Guihai; Li, Xingfu
Abstract
For a set S subset of V(G) in a network G, the Steiner distance d(G)(S) of S is the minimum size among all connected subnetworks whose vertex sets contain S. The Steiner k-eccentricity epsilon(kappa) (v) of a vertex v of G is the maximum Steiner distance among all k-vertex set S which contains the vertex v, i.e., s k (v) = max{d(S) vertical bar S subset of V(G), vertical bar S vertical bar = kappa, v is an element of S}. Based on Steiner keccentricity, the connective Steiner k-eccentricity index is introduced. As a newly structural invariant, some properties of the connective Steiner 3-eccentricity index are investigated. Firstly we present an O(n(2))-polynomial time algorithm to calculate the connective Steiner 3-eccentricity index of trees. Secondly some optimal problems among some network classes are discussed. As its application, finally we consider the network similarity measure based on the connective Steiner 3-eccentricity index. By two different methods, we study its advantages. Numerical results show that the measure based on the connective Steiner 3-eccentricity index has more advantages than the ones based on other topological indices (graph energy, Randic index, the largest adjacent eigenvalue, the largest Laplacian eigenvalue). (C) 2020 Elsevier Inc. All rights reserved.