The Calculation of Polar Surface Area from First Principles: An Application of Quantum Chemical Topology to Drug Design

The study of EGFR-ligand complex electron property relationship with biological activity

The present investigation grounded on estimation of electron properties of the structures of EGFR proteins-ligand complexes using our laboratory-developed methodology AlteQ approach, which describes the molecular electron density of the complex in space for a certain point in three-dimensional coordinates. Briefly, the system embodies molecular electron density as a sum of Slater's type atomic increments of the molecular system. Further, using this methodology, we calculated different electron characteristics of selected EGFR protein-ligand complexes and established the relationship between different electron properties with their experimental pharmacological activity value (pIC₅₀). The study suggested that EGFR inhibitory activity has higher correlation with intermolecular contacts of H with pi-system of aromatic ring between protein and ligands. Therefore, this created model has impact to identify and design potential ligands against EGFR in anticancer drug discovery.Communicated by Ramaswamy H. Sarma.

Computational Drug Designing and Prediction Of Important Parameters Using in silico Methods- A Review

BACKGROUND

Computational or in silico studies are undertaken to assess the drug like properties of lead compounds. These studies help in fast prediction of relevant properties.

OBJECTIVE

Through this review, an effort is made to encapsulate some of the important parameters which should be met by a compound for it to be considered as a potential drug candidate along with an overview of automated softwares which can be used for making various predictions.

METHODS

Drug uptake, its absorption, evacuation and associated hazardous effects are important factors for consideration in drug designing and should be known in early stages of drug development. Several important physicochemical properties like molecular weight, polar surface area (PSA), molecular flexibility etc. have to be taken into consideration in drug designing. Toxicological assessment is another important aspect of drug discovery which predicts the safety and adverse effects of a drug.

RESULTS

Additionally, bioactivity scores of probable drug leads against various human receptors can also be predicted to evaluate the probability of them to act as a potential drug candidate. The in vivo biological targets of a molecule can also be efficiently predicted by molecular docking studies.

CONCLUSION

Some important software like iGEMDOCK, AutoDock, OSIRIS property explorer, Molinspiration, MetaPrint2D, admetSAR and their working methodology and principle of working have been summarized in this review.

Thermodynamics of selective serotonin reuptake inhibitors partitioning into 1,2-dioleoyl-sn-glycero-3-phosphocholine bilayers

Knowledge of thermodynamics of lipid membrane partitioning of amphiphilic drugs as well as their binding site within the membrane are of great relevance not only for understanding the drugs' pharmacology but also for the development and optimization of more potent drugs. In this study, the interaction between two representatives of selective serotonin reuptake inhibitors, including paroxetine and sertraline, and large unilamellar vesicles (LUVs) composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) was investigated by second derivative spectrophotometry and Fourier transform infrared spectroscopy (FTIR) to determine the driving force of the drug partitioning across lipid membranes. It was found that temperature increase from 25 to 42 °C greatly enhanced the partitioning of paroxetine and sertraline into DOPC LUVs, and sertraline intercalated into the lipid vesicles to a greater extent than paroxetine in the temperature range examined. The partitioning of both drugs into DOPC LUVs was a spontaneous, endothermic and entropy-driven process. FTIR measurements suggested that sertraline could penetrate deeply into the acyl tails of DOPC LUVs as shown by the considerable shifts in the lipid's CH₂ and C Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> O stretching modes induced by the drug. Paroxetine, however, could reside closer to the head groups of the lipid since its presence caused a larger shift in the PO₂⁻ bands of DOPC LUVs. The findings reported here provide valuable insights into the influence of small molecules' chemical structure on their molecular interaction with the lipid bilayer namely their possible binding sites within the lipid bilayer and their thermodynamics profiles of partitioning, which could benefit rational drug design and drug delivery systems.

Paroxetine and sertraline have the same thermodynamics profile of phospholipid bilayer partitioning but different location within the lipid bilayer.

Synthesis of Jacaranone-Derived Nitrogenous Cyclohexadienones and Their Antiproliferative and Antiprotozoal Activities

The cytotoxic and antiprotozoal activities of the phytoquinoide, jacaranone, and related compounds have been an ongoing topic in recent drug discovery. Starting from the natural product-derived cyclohexadienone scaffold, a series of nitrogen-containing derivatives were synthesized and subsequently evaluated for their antiproliferative and antiprotozoal activity. Anticancer potency was analyzed using different types of cancer cell lines: MDA-MB-231 breast cancer, CCRF-CEM leukemia, HCT-116 colon cancer, U251 glioblastoma, and, in addition, non-tumorigenic MRC-5 lung fibroblasts. Antiproliferative activities at micromolar concentrations could be shown. Antiprotozoal activity was assessed against Plasmodium falciparum NF54 and Trypanosoma brucei rhodesiense STIB900. For all compounds, selectivity indices (SI) were calculated based on assessed cytotoxicity towards L6 cells. In addition, the structure-activity-relationships and physicochemical parameters of these compounds are discussed.

Synthesis and antiprotozoal activities of new 3-azabicyclo[3.2.2]nonanes

Some antimalarial agents in use typically bear basic side chains as ligands. Such ligands were attached to the amino substituent of a bridgehead atom of already antiprotozoal active 3-azabicyclo[3.2.2]nonanes. Structure verification was done by NMR measurements. The new compounds were tested for their antiplasmodial and antitrypanosomal activities against Plasmodium falciparum K 1 (multiresistant) and Trypanosoma brucei rhodesiense as well as for their cytotoxicity against L6 cells. Their activities are compared to those of already prepared compounds and structure-activity relationships are discussed.

Modeling biophysical and biological properties from the characteristics of the molecular electron density, electron localization and delocalization matrices, and the electrostatic potential

The electron density and the electrostatic potential are fundamentally related to the molecular hamiltonian, and hence are the ultimate source of all properties in the ground- and excited-states. The advantages of using molecular descriptors derived from these fundamental scalar fields, both accessible from theory and from experiment, in the formulation of quantitative structure-to-activity and structure-to-property relationships, collectively abbreviated as QSAR, are discussed. A few such descriptors encode for a wide variety of properties including, for example, electronic transition energies, pK(a)'s, rates of ester hydrolysis, NMR chemical shifts, DNA dimers binding energies, π-stacking energies, toxicological indices, cytotoxicities, hepatotoxicities, carcinogenicities, partial molar volumes, partition coefficients (log P), hydrogen bond donor capacities, enzyme-substrate complementarities, bioisosterism, and regularities in the genetic code. Electronic fingerprinting from the topological analysis of the electron density is shown to be comparable and possibly superior to Hammett constants and can be used in conjunction with traditional bulk and liposolubility descriptors to accurately predict biological activities. A new class of descriptors obtained from the quantum theory of atoms in molecules' (QTAIM) localization and delocalization indices and bond properties, cast in matrix format, is shown to quantify transferability and molecular similarity meaningfully. Properties such as "interacting quantum atoms (IQA)" energies which are expressible into an interaction matrix of two body terms (and diagonal one body "self" terms, as IQA energies) can be used in the same manner. The proposed QSAR-type studies based on similarity distances derived from such matrix representatives of molecular structure necessitate extensive investigation before their utility is unequivocally established.

Synthesis, evaluation of anticancer activity and COMPARE analysis of N-bis(trifluoromethyl)alkyl-N'-substituted ureas with pharmacophoric moieties

A series of new synthesized N-bis(trifluoromethyl)alkyl-N'-substituted ureas have been tested in the National Cancer Institute (NCI, Bethesda, USA) by Program NCI-60 DTP Human Tumor Cell Line Screen at a single high dose (10(-5) M). COMPARE analysis has been carried out for all tested compounds. The tested compounds showed antitumor activity against individual cell lines. The most sensitive cell lines relative to the tested compounds are: 5 g Leukemia RPMI-8226 (GI% 52.7), Non-Small Cell Lung cancer HOP-92 (GI % 88.53), NCI-H522 (GI % 64.41), Melanoma UACC-62 (GI% 53.08), SK-MEL-5 (GI % 74.63), Breast cancer MDA-MB-468 (GI% 51.29), T-47D (GI % 65.1), 5b Leukemia K-562 (GI % 55.55), 7 m Leukemia HL-60(TB) (GI % 51.76).

Quantum mechanical polar surface area

A correlation has been established between the absorbed fraction of training-set molecules after oral administration in humans and the Quantum Mechanical Polar Surface Area (QMPSA). This correlation holds for the QMPSA calculated with structures where carboxyl groups are deprotonated. The correlation of the absorbed fraction and the QMPSA calculated on the neutral gas phase optimized structures is much less pronounced. This suggests that the absorption process is mainly determined by polar interactions of the drug molecules in water solution. Rules are given to derive the optimal polar/apolar ranges of the electrostatic potential.

What has polar surface area ever done for drug discovery?

Over the last decade, polar surface area (PSA) has become a ubiquitous term in medicinal and computational chemistry circles. This article charts the development of the increasingly efficient methods for the calculation of PSA before illustrating its usefulness through selected examples drawn from the medicinal chemistry literature. Consideration of PSA is shown to assist in the improvement of cellular potency, intestinal absorption and blood-brain barrier permeation or restriction to the peripheral circulation.

Investigation of the molecular surface area and volume: Defined and calculated by the molecular face theory

Based on the molecular face (MF) theory, the molecular face surface area (MFSA) and molecular face volume (MFV) are defined. For a variety of organic molecules and several inorganic molecules, the MFSA and MFV have been studied and calculated in terms of an algorithm of our own via the Matlab package. The MFV shows a very good linear relationship with the experimentally measured critical molar volume. It is also found that the MFSA and MFV have significant linear correlations with those of the commonly used hard-sphere model and the electron density isosurface.