Pharmacological activity and druggability are two pivotal factors in drug innovation, which are respectively determined by the microscopic structure and macroscopic property of a molecule. Since structural optimization consists in a molecular operation in the space with multi-dimensions, and there exists a body of uncertainties for transduction from in vitro activity into in vivo pharmacological response. It is necessary for early stage in lead optimization to evaluate compound quality or efficiency using a kind of metrics containing multi-parameters. On the basis of the describing parameters of activity and druggability, this overview deals with the roles of thermodynamic signatures and binding kinetics of drug-receptor interactions in optimizing quality of compounds, signifying the significance in optimization of microscopic structures for drug discovery.
Drug Design ; Drug Discovery ; methods ; Ligands ; Molecular Structure ; Pharmaceutical Preparations ; chemical synthesis ; chemistry ; Pharmacokinetics ; Pharmacology ; Protein Binding ; Receptors, Drug ; chemistry ; Structure-Activity Relationship ; Thermodynamics

Taking patient needs as the core and realizing clinical value as the guidance are the purpose and path of drug discovery. Whether the first-in-class drug or follow-on drugs are all to meet the demands of patients for drugs that are not treatable or more safe and effective. In order to realize clinical value, innovative drugs driven by basic biological research include three elements: understanding the molecular mechanism of pathogenesis; Grasping the microscopic features of the disease; clarifying the mechanism of action of drugs. The interrelation among the three is the translational medicine, and the medicinal chemistry plays an important role in the translations. That is, based on the results of basic research in biology/medicine, knowledge of the molecular mechanism of disease depends upon the establishment of various in vitro/in vivo models to find the key node and molecular regulation for the treatment of disease. Combined with the knowledge of gene deletion and variation, proteomics, epigenetics and other technologies, the molecular mechanism of disease provides multi-molecular information on the level of gene, proteins, enzymes, receptors, ion channels and signal transduction for molecular drug design. Insight into the microscopic characteristics of diseases would deepen the understanding of the molecular mechanism of the pathogenesis, as well as provide a feasible scientific path for the creation of new drugs. When the molecular mechanism of disease and the action mechanism of drugs are clarified, we have a deeper and wider understanding of the application of existing drugs (or active compounds), and may offer new ideas for drug design and application. In this translational process the medicinal chemistry plays a key role which requires medicinal chemists to break through the habitual thinking and working mode, backtracking (upstream) to basic research and its achievements and applying to the direction of creating new drugs in time, as well as paying attention to the clinical requirements (downstream) and implementing the specific content of the transformation process for the R&D of innovative drugs.

Artificial intelligence-aided drug discovery (AIDD) is a new version of computer-aided drug discovery (CADD). AIDD is featured in significantly promoting the performance of conventional CADD. AI markedly enhances the learning ability of CADD. In the 1960s, CADD was established from conventional QSAR approaches, which mainly used regression approaches to derive substructure-activity relationship for compounds with a common scaffold, and guide drug molecular design, figure out the binding features of drugs, and identify potential drug targets. Since the 1990s, structural biology has provided three-dimensional structures of drug targets, enabling drug discovery based on target structure (SBDD), fragment-based drug discovery (FBDD), and structure-based virtual screening (SBVS) with CADD approaches. In the past 30 years, many first in class (FIC) and best in class (BIC) drugs were discovered with CADD. Now, AIDD will further revolutionize CADD by reducing human interventions and mining big chemical and biological data. It is expected that AIDD will significantly enhance the abilities of CADD, virtual screening and drug target identification. This article tries to provide perspectives of CADD and AIDD in medicinal chemistry with case studies.

The binding of small molecule drugs to targets is mostly through non-covalent bonds, and hydrogen bond, electrostatic, hydrophobic and van der Waals interactions function to maintain the binding force. The more these binding factors lead to strong bindings and high activities. However, it is often accompanied by the increase of molecular size, resulting in pharmacokinetic problems such as membrane penetration and absorption, as well as metabolism, which ultimately affects the drug success. Fragment-based drug discovery (FBDD) is to screen high-quality fragment library to find hits. Combine with structural biology, FBDD generates lead compounds by means of fragment growth, linking and fusion, and finally drug candidates by the optimization operation. During the value chain FBDD is closely related to structure-based drug discovery (SBDD). In this paper, the principle of FBDD is briefly described by several launched drugs.

The chemically induced proximity (CIP) in biological realm is an important way to maintain the function of organism and cells. In recent years, CIP has been paid attention to and applied in the field of bio-medicines. Molecular glue and PROTAC are widely investigated for the treatment of tumors and immunopathy. Based upon the CIP principle molecular glue and PROTAC promote two proteins to approach each other, induce the complementary binding to triads, and then degrade the target protein or regulate functions. Different from conventional drugs, molecular glue acts as a catalyst, which induces two proteins to approach, bind and ubiquitinate, without taking part in the subsequent degradation process, so it can theoretically function in an infinite cycle. In this article, the development process, structural characteristics and functional characteristics of some molecular glues in clinical trials are briefly discussed from the viewpoint of medicinal chemistry.

Small molecule drugs comprise multi-dimensional features, and drug creation has to meet requirements such as safety, effectiveness, stability, controllability, and patient compliance. These attributes can be summarized as pharmacological activity and druglikeness, which are implicit in the chemical structure of the drug. Pharmacological activity and adverse reactions are caused by the interaction between drug molecules and on-target or off-target protein. The microstructure of the drug determines the activity/toxicity intensity and selectivity. Pharmacokinetic and physicochemical properties are related to the macroscopic properties of the drug, and the microstructure and macroscopic properties are intertwined and integrated into the molecular structure. Conception and construction of bifunctional molecules are one of routes to achieve "unification of micro and macro" and structurally straighten out the relationship between pharmacodynamics-pharmacokinetics, drug efficacy-adverse reactions (selectivity). This article takes drugs that have been successfully marketed or under clinical trials as examples to explain the structural characteristics of bifunctional molecules from the viewpoint of medicinal chemistry. The productive technical methods include antibody-drug conjugate, proteolysis-targeting chimeras, molecular glues, peptide modifications, and so on. In addition, this overview also classifies covalently binding drugs, transition-state analogs, and prodrugs into the category of bifunctional molecules, emphasizing the importance of bifunctional groups in molecular design and structure optimization.

Although small molecule drugs (SMD) are still mainstream for the treatment of diseases, large molecule biologicss of many advantages, pose a challenge to the further discovery and use of SMD. The advantages of SMD are the convenience of oral administration and good patient compliance. However, the challenge with SMD is to integrate the PD, PK, selectivity and safety into a chemical structure. Because of their small size and surface area they often bind to various proteins, and off-target actions can cause adverse reactions. In this sense, selectivity is critical. Based upon target as the core to construct a chemical structure, it is necessary to consider the requirements of all the attributes, but achievement of the full-dimensional optimization is difficult. Modern drug discovery has been greatly enhanced by molecular biology and structural biology, and new strategies and technologies have emerged, which have created many successful medicines. For example, under the guidance of structural biology, covalent binding drugs connect moderate "electrophilic warheads" to the appropriate positions of molecules, and upon binding to their targets the electrophiles are irreversibly linked to the target by covalent bonds. Molecular biology can be directly applied to the development of antibody-coupled drugs (ADC). The antibody (A) acts as a carrier and a guide (for PK), and carries toxic molecules (D) into cancer cells, thus playing a killing role (for PD). The separate pharmacodynamic and pharmacokinetic entities are coupled (C) by linkers. PROTACs are also bifunctional molecules, which recruit a target protein and ubiquitin ligase E3 to form a ternary complex, which then acts as a catalyst to ubiquitinate the target protein and lead to degradation by the proteasome. In addition, in recent years, the combination of two fixed-dose drugs has improved selectivity, safety, and long-term benefit with many severe diseases, and can be regarded as an innovative strategy of physical combination. This review discusses some successful examples to briefly present the principles from the perspective of medicinal chemistry and therapeutic application.

Hits, leads and drug candidates constitute three millstones in the course of drug discovery and development. The definition of drug candidates is a critical point in the value chain of drug innovation, which not only differentiates the research and development stages, but more importantly, determines the perspective and destiny of the pre-clinical and clinical studies. All outcomes from the development stage are actually attributed to the chemical structure of candidates. The quality of candidates, however, is restricted by the drug-likeness of lead compounds, which in turn is decided by the characteristics of hits. The hit-to-lead is to provide a promising and druggable structure for further development, whereas the optimization of lead compounds is a process to transform an active compound into a drug, which in essence is molecular manipulation in multi-dimensional space related to pharmacodynamic, pharmacokinetic, physico-chemical, and safety properties. This review discusses the strategic principles in hit discovery, lead identification and optimization, as well as drug candidate definition with practical examples.
Animals ; Drug Design ; Drug Evaluation, Preclinical ; methods ; Drug Industry ; methods ; Humans ; Molecular Structure ; Pharmaceutical Preparations ; chemistry

The interaction of a drug with the organism involves both the disposition of a drug by the organism and the action of a drug on the organism. The disposition of various exogenous substances, including drugs, complies with general rules. The underlying physical and chemical changes to different drugs in view of time and space, i. e. pharmacokinetics, share common characteristics, that is the tout ensemble of a molecule and its macroscopic properties convey direct effect on the pharmacokinetic behavior as the tendency and consequence of biological evolution. The action of a drug on the organism, on the other hand, implicates the physico-chemical binding of a drug molecule to the target protein, which induces pharmacological and toxicological effects. The biological reactions, no matter beneficial or adverse, are all specific and individual manifestation of the drug molecule and determined by the interactive binding between definitive atoms or groups of the drug molecule and the macromolecular target in three-dimension. Such critical atoms, groups, or fragments responsible for the interaction reflect the microscopic structures of drug molecules and are called pharmacophore. In this context, a drug molecule is presumed as an assembly of macroscopic property and microscopic structure, with the macroscopic properties determining the absorption, distribution, metabolism and elimination of drugs and the microscopic structure coining pharmacological action. The knowledge of the internal relationship between macroscopy/microscopy and PK/PD conduces to comprehension of drug action and guides molecular drug design, because this conception facilitates the identification of structural features necessary for biological response, and the determination of factors modulating the physico-chemical and pharmacokinetic properties. The factors determining macro-properties include molecular weight, solubility, charge, lipophilicity (partition), and polar surface area, etc., which are destined by molecular scaffolds and/or side chain(s) apart from pharmacophore. The features of micro-structures contributing to specific activity contain hydrogen bonding donor and acceptor, positive and negative charge centers, hydrophobic centers and centers of aromatic rings. Different combinations and spacial arrangements of these features determine the distinct activity presented. The macro-property and micro-structure are integrated into a single molecule, and are inseparable. The macro-property reflects overall contribution of atoms and groups in the micro-structure. On the other hand, structural changes aimed to adjust macroscopic property usually alter the relative position of the microscopic structure. The goal of molecular drug design is to integrate the macroscopic and microscopic factors in optimized manner. In the early stage of molecular design, both macroscopic property and microscopic structure should be considered to make pharmacodynamics, pharmacokinetics, and physico-chemical properties in optimal match. Therefore, it required the existence of structural overlapping among acceptable pharmacokinetics, visible developing potential and specific pharmacodynamics. The larger the scope of overlapping, the higher the possibility to be a drug.
Databases, Genetic ; Drug Design ; Models, Molecular ; Molecular Structure ; Molecular Weight ; Pharmaceutical Preparations ; chemical synthesis ; chemistry ; Pharmacokinetics ; Solubility ; Structure-Activity Relationship

Pharmacological activity and druggability are two essential factors for drug innovation. The pharmacological activity is definitely indispensable, and the druggability is destined by physico-chemical, biochemical, pharmacokinetic and safety properties of drugs. As secondary metabolites of animals, plants, microbes and marine organisms, natural products play key roles in their physiological homeostasis, self-defense, and propagation. Natural products are a rich source of therapeutic drugs. As compared to synthetic molecules, natural products are unusually featured by structural diversity and complexity more stereogenic centers and fewer nitrogen or halogen atoms. Naturally active substances usually are good lead compounds, but unlikely meet the demands for druggability. Therefore, it is necessary to modify and optimize these structural phenotypes. Structural modification of natural products is intent to (1) realize total synthesis ready for industrialization, (2) protect environment and resources, (3) perform chemical manipulation according to the molecular size and complexity of natural products, (4) acquire novel structures through structure-activity relationship analysis, pharmacophore definition, and scaffold hopping, and (5) eliminate unnecessary chiral centers while retain the bioactive configuration and conformation. The strategy for structural modification is to increase potency and selectivity, improve physico-chemical, biochemical and pharmacokinetic properties, eliminate or reduce side effects, and attain intellectual properties. This review elucidates the essence of natural products-based drug discovery with some successful examples.
Biological Products ; chemical synthesis ; chemistry ; Drug Design ; Drug Discovery ; Drug Stability ; Humans ; Molecular Structure ; Solubility ; Structure-Activity Relationship