Computational design of novel cyclic urea as HIV-1 protease inhibitor

A series of novel cyclic urea molecules 5,6-dihydroxy-1,3-diazepane-2,4,7-trione as HIV-1 protease inhibitors were designed using computational techniques. The designed molecules were compared with the known cyclic urea molecules by performing docking studies, calculating their ADME (Absorption, Distribution, Metabolism, and Excretion) properties and protein ligand interaction energy. These novel molecules were designed by substituting the P ₁/P′ ₁ positions (4 ^th and 7 ^th position of 1, 3-diazepan-2-one) with double bonded oxygens. This reduces the molecular weight and increases the bioavailability, indicating better ADME properties. The docking studies showed good binding affinity towards HIV-1 protease. The biological activity of these inhibitors were predicted by a model equation generated by the regression analysis between biological activity (log 1/K ⁱ ) of known inhibitors and their protein ligand interaction energy. The synthetic studies are in progress.      

Pharmacophore modelling,atom-based 3D-QSAR generation and virtual screening of molecules projected for mPGES-1 inhibitory activity

COX-2 inhibitors exhibit anticancer effects in various cancer models but due to the adverse side effects associated with these inhibitors, targeting molecules downstream of COX-2 (such as mPGES-1) has been suggested. Even after calls for mPGES-1 inhibitor design, to date there are only a few published inhibitors targeting the enzyme and displaying anticancer activity. In the present study, we have deployed both ligand and structure-based drug design approaches to hunt novel drug-like candidates as mPGES-1 inhibitors. Fifty-four compounds with tested mPGES-1 inhibitory value were used to develop a model with four pharmacophoric features. 3D-QSAR studies were undertaken to check the robustness of the model. Statistical parameters such as r² = 0.9924, q² = 0.5761 and F test = 1139.7 indicated significant predictive ability of the proposed model. Our QSAR model exhibits sites where a hydrogen bond donor, hydrophobic group and the aromatic ring can be substituted so as to enhance the efficacy of the inhibitor. Furthermore, we used our validated pharmacophore model as a three-dimensional query to screen the FDA-approved Lopac database. Finally, five compounds were selected as potent mPGES-1 inhibitors on the basis of their docking energy and pharmacokinetic properties such as ADME and Lipinski rule of five.     

SAMPL7 blind challenge: quantum–mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules

The physicochemical properties of a drug molecule determine the therapeutic effectiveness of the drug. Thus, the development of fast and accurate theoretical approaches for the prediction of such properties is inevitable. The participation to the SAMPL7 challenge is based on the estimation of logP coefficients and pK_a values of small drug-like sulfonamide derivatives. Thereby, quantum mechanical calculations were carried out in order to calculate the free energy of solvation and the transfer energy of 22 drug-like compounds in different environments (water and n-octanol) by employing the SMD solvation model. For logP calculations, we studied eleven different methodologies to calculate the transfer free energies, the lowest RMSE value was obtained for the M06L/def2-TZVP//M06L/def2-SVP level of theory. On the other hand, we employed an isodesmic reaction scheme within the macro pK_a framework; this was based on selecting reference molecules similar to the SAMPL7 challenge molecules. Consequently, highly well correlated pK_a values were obtained with the M062X/6–311+G(2df,2p)//M052X/6–31+G(d,p) level of theory.

     

Nonlocal energy density functionals: Models plus some exact general results

Holas and March (Phys Rev 1995 A51, 2040) gave a formally exact expression for the force ??V_xc( r )/? r associated with the exchange‐correlation potential V_xc( r ) of density functional theory. This forged a precise link between first‐ and second‐order density matrices and V_xc( r ). Here models are presented in which these low‐order matrices can be related to the ground‐state electron density. This allows nonlocal energy density functionals to be constructed within the framework of such models. Finally, results emerging from these models have led to the derivation of some exact “nuclear cusp” relations for exchange and correlation energy densities in molecules, clusters, and condensed phases. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

3D-QSAR (CoMFA,CoMSIA, HQSAR and topomer CoMFA), MD simulations and molecular docking studies on purinylpyridine derivatives as B-Raf inhibitors for the treatment of melanoma cancer

As per the World Health Organization (WHO), cancer is the second most leading cause of death after cardiovascular diseases in worldwide with around 9.88 million total new cases and 1.08 million were observed due to skin cancer in 2018. Amongst two types of skin cancer, progression of melanoma cancer is increasing day by day due to the environmental changes than non-melanoma cancer. Most of B-Raf mutation, specifically B-RafV600E, is responsible for the progression of the melanoma cancer. Here, various 3D-QSAR techniques like comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), molecular hologram QSAR (HQSAR) and topomer CoMFA were used to design novel B-Raf inhibitors by using 28 synthetic B-Raf inhibitors. Except for topomer CoMFA model, remaining models were generated by three different alignment methods in which distil-based alignment method was found best and gave prominent statistical values. After performing N-fold statistical validation, in CoMFA, q², r² and r²_pred values were found to be 0.638, 0.969 and 0.848, respectively. Similarly, q², r² and r²_pred values were found to be 0.796, 0.978 and 0.891 in CoMSIA (SHD) and 0.761, 0.973 and 0.852 in CoMSIA (SH) by N-fold statistical validation. In HQSAR analysis, statistical values were found for q² as 0.984, r² as 0.999 and r²_pred as 0.634 with 97 as best hologram length (BHL). The results of topomer CoMFA showed the q² value of 0.663 and the r² value of 0.967. Important features of purinylpyridine were identified by contour map analysis of all 3D-QSAR techniques, which could be useful to design the novel molecules as B-Raf inhibitors for the treatment of melanoma cancer.

     

Thermal dissociation and recombination of alkyl and haloalkyl peroxynitrates: An SACM modelling study

Recent experimental results on the thermal decomposition and the reverse recombination of alkyl and haloalkyl peroxynitrates are modelled with an SACM formalism. The molecules RO₂NO₂ with R = CH₃, CF₃, CF₂Cl, CFCl₂, CCl₃, and C₂H₅ are considered. Detailed and simplified reduced falloff expressions are compared. Limiting low (??_o) and high pressure (??_x) rate constants, such as derived from a fit of these falloff expressions to the experiments, are compared with absolute predictions, based on general knowledge about energy transfer (〈ΔE〉 in ??_o) and on a recently proposed simple SACM estimate for ??_x. The analysis also allows for a derivation of the bond energies of the mentioned molecules.     

The role of kinetic energy in chemical binding

The wavefunctions and various partitions of the energy are examined for a variety of small molecules (H₂, H₃, H₄, HeH, HeH₂, He₂, LiH, and BH) in order to isolate the factors crucial for bond formation. We find that a natural partition of the energy leads to the conclusion that the crucial factor is the exchange, or nonclassical, part of the kinetic energy, T ^x. The change in T ^xupon pushing the atoms towards one another is the dominant term in the binding energy; it is negative when the resulting molecule is stable and positive when it is unstable. We show that T ^x is related to the interference kinetic energy considered by Ruedenberg.

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Zusammenfassung Die Wellenfunktionen und verschiedene Zerlegungen der Energie werden für eine Reihe kleiner Moleküle untersucht (H₂, H₃, H₄, HeH, HeH₂, He₂, LiH und BH), um die Faktoren zu finden, die für die Bindungsbildung ausschlaggebend sind. Die natürliche Zerlegung der Energie läßt die Folgerung zu, daß der bestimmende Faktor der Austauschanteil T ^x(oder nichtklassische Anteil) der kinetischen Energie ist. Die Änderung von T ^xbeim Zusammenführen der Atome ist der dominierende Term für die Bindungsenergie; er ist negativ, wenn das resultierende Molekül stabil ist, und positiv, falls es instabil ist. Es wird gezeigt, daß T ^x im Zusammenhang zum Wechselwirkungsanteil der kinetischen Energie nach Ruedenberg steht.

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Partially supported by a grant (GP-15423) from the National Science Foundation. This paper is based on a portion of the PhD thesis (California Institute of Technology, 1970) by CWW.

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National Science Foundation Predoctoral Trainee.

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Alfred P. Sloan Foundation Research Fellow.

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Contribution No. 3917.     

Influence of decoration with Si and Ge atoms on the sensitivity of boron nitride nanocone towards temozolomide anticancer drugs

The nature of intermolecular interactions between BN nanocones (BNNCs) and temozolomide (TMZ) drug has been described by using Wiberg bond index (WBI) and natural bond orbital (NBO) analyses. The adsorption energy of TMZ on the Si and Ge-decorated BNNCs were calculated to be about ??17.64 and ??16.47 kcal mol^?1, respectively. Also, after TMZ adsorption, the band gap energy (E_g) value of Si (Ge)-decorated BNNCs has reduced significantly by about 51.41% (50.99%), increasing the electrical conductivity, while the E_g value of pristine BNNCs was slightly reduced after TMZ adsorption. It indicates that the Si (Ge)-decorated BNNCs compared to pristine state could be more appropriate candidate for TMZ detection and may be used in the electronic sensors. Furthermore, the work function of Si (Ge)-decorated BNNCs is influenced by the TMZ adsorption, and the work function of decorated and pristine BNNCs is reduced by about 32.42% and 4.15%, respectively. The nature of interactions between TMZ and BNNCs is noncovalent based on the WBI and NBO results.

     

Molecular weight distribution in random crosslinking of polymer chains

The molecular weight distribution (MWD) of crosslinked polymer molecules formed during polymeric network formation is the sum of the fractional MWDs containing 0, 1, 2, 3, … crosslinkages. The MWD for polymer molecules containing ?? crosslinkages is investigated for the random crosslinking of polymer chains whose initial MWD is given by the Schulz-Zimm distribution. For a very narrow initial MWD, each fractional MWD with ?? = 0, 1, 2, … is independent and a multimodal distribution is obtained for the whole distribution. When the initial MWD is uniform, the average crosslinking density within the polymer fraction whose degree of polymerization is r, ρ_r is simply given by ρ_r = ρ_gel,c – 2/r irrespective of the extent of crosslinking reaction where ρ_gel,c is the crosslinking density within gel fraction at the gel point. On the other hand, the MWDs with ?? crosslinkages overlap each other with different ?? values significantly for the broader initial distributions, and ρ_r increases with the progress of crosslinking reactions. The value of ρ_r increases with increasing r but levels off asymptotically at large r. The average crosslinking density of polymer molecules containing ?? crosslinkages ρ_?? is an increasing function of k but soon reaches a plateau; sooner for the broader initial MWDs. For ?? ≥ 1, ρ_?? is always larger than the average crosslinking density of the whole reaction system ρ in the pregelation period, i.e., in terms of the crosslinking density, the difference between polymer molecules with and without crosslinkage is most significant. In general, the average crosslinking density ρ, which is convenient to use in describing the nature of the whole reaction system, cannot be considered as a characteristic degree of crosslinking for polymer molecules containing at least one crosslinkage. Consideration of the bivariate distribution of r and k reveals important aspects of the polymeric network formation that have been obscured in the conventional theories in which the averages including linear polymers are solely considered. © 1995 John Wiley & Sons, Inc.     

Enhanced nonlinear optical properties of porphyrin with an extended π-conjugated bridge

In this work, a series of molecules with an extended π-conjugated bridge have been theoretically designed based on porphyrin, where -(CH=CH)_n- (n = 1–4, 8, 12) chain is served as an extended π-conjugated bridge. It is found that all molecules exhibit large energy gaps in the range of 3.484–4.151 eV for porphyrin-(CH=CH)_n-NH₂, and 3.624–4.250 for porphyrin-(CH=CH)_n-NO₂. The maximum absorption wavelengths of all molecules show a red shift trend with increasing -(CH=CH)_n- length, which leads to small transition energy. It is observed that long chain brings these molecules the large first hyperpolarizability, which are 1.04 × 10⁵ au for porphyrin-(CH=CH)₁₂-NH₂, 1.26×10⁵ au for porphyrin-(CH=CH)₁₂-NO₂. Moreover, compared with -(CH=CH)_n-NH₂ with the same chain length, -(CH=CH)_n-NO₂ chain can achieve larger nonlinear optical response. It is hoped that the research in this paper can provide a new strategy for the experimental design of nonlinear optical materials.

     

Dissociation, solvation, and dynamics of HBr in small water clusters

The dissociation of hydrogen bromide in a small water cluster (H₂O)_n (n=3–5) has been studied with quantum chemical methods. The dynamics of dissociation was followed by classical molecular dynamics, and stationary points were studied in order to compute the free energy change associated with the ionization process. The nudged elastic band method was used to map out the energy profile of the reaction paths. The results show that HBr can dissociate in the presence of just four water molecules if they are in the correct configuration.The relation of our results to recent experiments is discussed.     

Configuration interaction matrix elements for atoms using permutation group algebra

A procedure is described for the efficient evaluation of the energy matrix elements necessary for atomic configuration-interaction calculations. With the orbital configurations of an N electron system in spin state S written as the irreducible representations [2^1/2N?S, 1^2S] of the permutation group S( N ), it is possible to evaluate readily the energy matrix elements of a spin-free Hamiltonian expressed in terms of the generators of the unitary group. We show how the use of angular momentum ladder operators permits the effective generation of a basis of eigenstates of ??², ??_z as well as ??² and ??_z, for which the energy matrix elements may be evaluated with ease.     

Molecular dynamics simulation of the interaction between methyl benzotriazole and Cu2O crystal

In circulating water system , methyl benzotriazole (TTA) is one of the common corrosion inhibitors for copper. But the inhibition mechanisms have not been clearly understood so far. In different number of water molecules, the interaction between TTA and Cu₂O (copper surface) was investigated with molecular dynamics (MD) method. The results showed that the MD simulation result with water was more consistent with the experiment results. In different number of water molecules, the sequence of the interaction energies between TTA and Cu₂O (001) was ? E ₁ (150H₂O) > ? E ₁(200H₂O) > ? E ₁(100H₂O) > ? E ₁(50H₂O) > ? E ₁(0H₂O). The number of water molecules had an important influence on the interaction between corrosion inhibitors and Cu₂O crystal. From non‐bond energy and pair correlation functions, the interaction energies of the model system were mainly contributed by the non‐bond interaction. Strong adsorption could be raised by the Coulomb interaction between the negatively charged functional groups in TTA and the positive copper ions in the Cu₂O (001) face, and further interaction between aggressive media and copper could be restricted. So, copper corrosion could be avoided. Chemical bonds and non‐bond interactions were formed between TTA and Cu₂O (001) in different number of water molecules. Water molecules could not be ignored during the MD simulation, too. The results obtained here may provide theoretical supports for developing new corrosion inhibitors.     

Rapid discovery of inhibitors of <Emphasis Type="Italic">Toxoplasma gondii</Emphasis> using hybrid structure-based computational approach

Toxoplasma (T.) gondii, the causative agent of toxoplasmosis, is a ubiquitous opportunistic pathogen that infects individuals worldwide, and is a leading cause of severe congenital neurologic and ocular disease in humans. No vaccine to protect humans is available, and hypersensitivity and toxicity limit the use of the few available medicines. Therefore, safer and more effective medicines to treat toxoplasmosis are urgently needed. Using the Hybrid Structure Based (HSB) method, we have previously identified small molecule inhibitors of P. falciparum that seem to target a novel protein–protein interaction between the Myosin tail interacting protein and myosin light chain. This pathway has been hypothesized to be involved in invasion of host erythrocytes by the parasite and is broadly conserved among the apicomplexans. Guided by similar computational drug design approaches, we investigated this series of small molecules as potential inhibitors of T. gondii. Compound C3-21, identified as the most active inhibitor in this series, exhibited an IC₅₀ value ~500 nM against T. gondii. Among the 16 structural analogs of C3-21 tested thus far, nine additional compounds were identified with IC₅₀ values <10.0 μM. In vitro assays have revealed that C3-21 markedly limits intracellular growth of T. gondii tachyzoites, but has no effect on host cell human foreskin fibroblasts (HFF) at concentrations more than a log greater than the concentration that inhibits the parasites.     

Hydrogen‐Bond Cooperative Effects in Small Cyclic Water Clusters as Revealed by the Interacting Quantum Atoms Approach

The cooperative effects of hydrogen bonding in small water clusters (H₂O)_n (n=3–6) have been studied by using the partition of the electronic energy in accordance with the interacting quantum atoms (IQA) approach. The IQA energy splitting is complemented by a topological analysis of the electron density (ρ( r )) compliant with the quantum theory of atoms‐in‐molecules (QTAIM) and the calculation of electrostatic interactions by using one‐ and two‐electron integrals, thereby avoiding convergence issues inherent to a multipolar expansion. The results show that the cooperative effects of hydrogen bonding in small water clusters arise from a compromise between: 1) the deformation energy (i.e., the energy necessary to modify the electron density and the configuration of the nuclei of the isolated water molecules to those within the water clusters), and 2) the interaction energy (E_int) of these contorted molecules in (H₂O)_n. Whereas the magnitude of both deformation and interaction energies is enhanced as water molecules are added to the system, the augmentation of the latter becomes dominant when the size of the cluster is increased. In addition, the electrostatic, classic, and exchange components of E_int for a pair of water molecules in the cluster (H₂O)_n?1 become more attractive when a new H₂O unit is incorporated to generate the system (H₂O)_n with the last‐mentioned contribution being consistently the most important part of E_int throughout the hydrogen bonds under consideration. This is opposed to the traditional view, which regards hydrogen bonding in water as an electrostatically driven interaction. Overall, the trends of the delocalization indices, δ(Ω,Ω′), the QTAIM atomic charges, the topology of ρ( r ), and the IQA results altogether show how polarization, charge transfer, electrostatics, and covalency contribute to the cooperative effects of hydrogen bonding in small water clusters. It is our hope that the analysis presented in this paper could offer insight into the different intra‐ and intermolecular interactions present in hydrogen‐bonded systems.     

Structure–activity relationships of diphenyl-ether as protoporphyrinogen oxidase inhibitors: insights from computational simulations

Protoporphyrinogen oxidase (PPO, EC 1.3.3.4), which has been identified as a significant target for a great family of herbicides with diverse chemical structures, is the last common enzyme responsible for the seventh step in the biosynthetic pathway to heme and chlorophyll. Among the existing PPO inhibitors, diphenyl-ether is the first commercial family of PPO inhibitors and used as agriculture herbicides for decades. Most importantly, diphenyl-ether inhibitors have been found recently to possess the potential in Photodynamic therapy (PDT) to treat cancer. Herein, molecular dynamics simulations, approximate free energy calculations and hydrogen bond energy calculations were integrated together to uncover the structure–activity relationships of this type of PPO inhibitors. The calculated binding free energies are correlated very well with the values derived from the experimental k _i data. According to the established computational models and the results of approximate free energy calculation, the substitution effects at different position were rationalized from the view of binding free energy. Some outlier (e.g. LS) in traditional QSAR study can also be explained reasonably. In addition, the hydrogen bond energy calculation and interaction analysis results indicated that the carbonyl oxygen on position-9 and the NO₂ group at position-8 are both vital for the electrostatic interaction with Arg98, which made a great contribution to the binding free energy. These insights from computational simulations are not only helpful for understanding the molecular mechanism of PPO-inhibitor interactions, but also beneficial to the future rational design of novel promising PPO inhibitors.     

Triazine-cored dendritic molecules containing multiple o-carborane clusters

A series of C₃-symmetricaltriazine-cored small dendritic molecules containing three to nine peripheral o-carborane clusters were synthesized through Cu(I)-catalyzedazide–alkyne cycloaddition reactions. The newly synthesized molecules containing multiple o-carborane moieties were characterized using nuclear magnetic resonance and matrix-assisted laser desorption/ionization-time of flight mass spectral analysis. The biological evaluation of these three to nine cage dendrimers was performed using breast cancer cells (Michigan Cancer Foundation 7). All these dendritic compounds showed cytotoxicity toward breast cancer cells, and the toxicity increased as the number of peripheral o-carboranes increased. The 9-cage molecule showed the highest cytotoxicity, and the half maximal inhibitory concentration (IC₅₀) value was found to be 80.67 ng/ml. Its cytotoxicity was significantly higher than the common chemotherapy agent cisplatin. As expected, the boron-richo-carborane-appended molecules showed high thermal stability. The thermal stability increased as the number of peripheral o-carborane moieties increased.     

Discovery of novel IDO1 inhibitors via structure-based virtual screening and biological assays

Indoleamine 2,3-dioxygenase 1 (IDO1) is a heme-containing enzyme that catalyzes the first and rate-limiting step in catabolism of tryptophan via the kynurenine pathway, which plays a pivotal role in the proliferation and differentiation of T cells. IDO1 has been proven to be an attractive target for many diseases, such as breast cancer, lung cancer, colon cancer, prostate cancer, etc. In this study, docking-based virtual screening and bioassays were conducted to identify novel inhibitors of IDO1. The cellular assay demonstrated that 24 compounds exhibited potent inhibitory activity against IDO1 at micromolar level, including 8 compounds with IC₅₀ values below 10 μM and the most potent one (compound 1) with IC₅₀ of 1.18?±?0.04 μM. Further lead optimization based on similarity searching strategy led to the discovery of compound 28 as an excellent inhibitor with IC₅₀ of 0.27?±?0.02 μM. Then, the structure–activity relationship of compounds 1, 2, 8 and 14 analogues is discussed. The interaction modes of two compounds against IDO1 were further explored through a Python Based Metal Center Parameter Builder (MCPB.py) molecular dynamics simulation, binding free energy calculation and electrostatic potential analysis. The novel IDO1 inhibitors of compound 1 and its analogues could be considered as promising scaffold for further development of IDO1 inhibitors.

     

Luciferase‐Induced Photouncaging: Bioluminolysis

Bioluminescence resonance energy transfer (BRET) has been widely used for studying dynamic processes in biological systems such as protein–protein interactions and other signaling events. Aside from acting as a reporter, BRET can also turn on functions in living systems. Herein, we report the application of BRET to performing a biorthogonal reaction in living cells; namely, releasing functional molecules through energy transfer to a coumarin molecule, a process termed bioluminolysis. An efficient BRET from Nanoluc‐Halotag chimera protein (H‐Luc) to a coumarin substrate yields the excited state of coumarin, which in turn triggers hydrolysis to uncage a target molecule. Compared to the conventional methods, this novel uncaging system requires no external light source and shows fast kinetics (t_1/2<2 min). We applied this BRET uncaging system to release a potent kinase inhibitor, ibrutinib, in living cells, highlighting its broad utility in controlling the supply of bioactive small molecules in vivo.