The Drug Discovery Process

Drug discovery is at the core of medicinal chemistry. Many medicinal chemists will tell you that their lifelong dream is to see a molecule they invented put into humans as a therapeutic treatment. There are certainly many diseases and conditions for which the currently available treatment options are too expensive, mostly ineffective or not even available. Therefore, there is always a need for scientists who want to apply their talent and hard work to discovering new drugs. It is not easy: by many estimates the cost to bring a molecule from the idea stage into an FDA approved drug sold in drug stores is about $1.2 billion and takes 10-12 years. Most of this money is spent at the tail end of the drug discovery process when pharmaceutical companies are performing large-scale clinical trials on the most promising candidate molecules. The path to get to that stage has many interesting and challenging roles for medicinal chemists – starting with an idea that a small chemical might modulate the activity of a biomacromolecule in such a way as to cause a pharmacological response. That idea is the basis for what is called “target validation”, i.e., proving that a specific biological molecule is worth pursuing as the object of drug discovery. The identification of active compounds proceeds from “hits” to “leads” to “candidates” as more and more effort is put into improving or optimizing their efficacy and physiochemical properties. The topics listed below describe some of the disease-specific projects and state-of-the-art techniques that VCU medicinal chemists are working on in their world-class research programs.

Allosteric Interactive Drugs

Allosteric proteins regulate some of the most important biochemical pathways in organisms. Identification of allosteric binding site modulators have gained increased attention for their potential to be developed as selective therapeutic agents with fewer side effects. VCU medicinal chemists have a very long history of exploring the structure, function and biochemistry of hemoglobin, which is the most famous allosteric protein. Martin Safo’s group has continued this interest in understanding the structures, functions and regulatory mechanisms of the allosteric binding sites of hemoglobin, but has also studied pyruvate kinase, and 2,3-DPG mutase with respect to their potential as drug targets for a range of diseases. Using structure-based drug design, several hemoglobin allosteric effectors with ideal oxygen modulating properties potentially useful for the treatment of hypoxic diseases and sickle cell anemia have been discovered including 5-hydroxymethylfurfural (5-HMF), a safe, potent, and highly effective anti-sickling agent. 5-HMF was one of the first molecules to enter the NIH Therapeutics for Rare and Neglected Diseases program. The group of Umesh Desai is developing allosteric regulators of coagulation proteases such as thrombin, factor Xa, factor IXa, and factor XIa. Here, allosterism arises from cooperativity between the heparin-binding site and the active sites of these proteases. Small molecule glycosaminoglycan (GAG) mimetics that induce either full or partial inhibition of protease activity resulting in anticoagulation effects have been discovered. In vivo this translates to antithrombotic activity.

Allosteric Interactive Drugs

Anticoagulants and Enzyme Mechanisms

Natural glycosaminoglycans (GAGs), such as heparin (H) and heparan sulfate (HS), interact with an anion-binding exosite “2” on most coagulation proteases. Classic evidence of this is that longer chains of heparin accelerate the reaction of antithrombin with thrombin, factor Xa, factor IXa and factor XIa through the “bridging” mechanism. While these exosites are typically thought of as similar, structurally they are quite distinct (see Figure). Each consists of several basic lysine and arginine groups; their number is not fully conserved nor is their location absolutely identical across such proteases. Also, while each exosite 2 has subdomains of considerable hydrophobicity, these subdomains are very diverse in size, location and scope across the proteases. Umesh Desai and his group have shown that these microscopic differences likely ‘discriminate’ H/HS sequences and exploring whether specific coagulation proteases can be selectively targeted by exploiting the microscopic electrostatic and hydrophobic differences between them. This ‘dual element design strategy’ has already led to the design of highly selective agents such as novel antithrombotic agents that selectively target each of the coagulation proteases.

Anticoagulants and Enzyme Mechanisms

Anti-Cancer Therapeutics

Progress made in the 21st century study of cancer, including studies of the human genome, personalized approaches to diagnosis and treatment, and the development of completely new therapeutic mechanisms for treatment, have turned cancer from a death sentence into a manageable disease that may one day soon be “cured”. The current challenge in the field is the development of cancer-selective or tumor-selective drug for the treatment of both hematological cancers and solid tumors. The main goal for these therapies is to treat and kill only the tumor cells without causing any toxicity to normal, healthy cells or tissues in the body. Keith Ellis leads a team of investigators working to discover potent and selective inhibitors for the oncogenic transcription co-regulator CtBP, which is a novel target for a tumor-selective therapy. The lead compound HIPP has been evaluated in animal models of colon cancer. Another cancer target, tubulin, has been explored with extensive SAR and computational studies by Glen Kellogg and his group. Umesh Desai has been working with a group at the McGuire VA Medical Center in developing glycosaminoglycan (GAG) mimetics as highly selective inhibitors of cancer stem cells (CSCs). Some of these molecules have been shown to be potent inhibitors of CSCs that inhibit cancer xenograft growth in mouse models.

Anti Cancer Therapeutics

Anti-HIV Therapeutics

AIDS no longer is a universally fatal disease to human society because very effective drug cocktail therapies have been developed and are currently being applied successfully. The current understanding of the virus evolved with the contributions of many disciplines, including some molecular modeling performed at VCU in the 1990s. It is important to realize, however, despite these very well publicized successes, that HIV infection still threatens the health and living conditions of AIDS patients and HIV carriers by invading the central nervous system, which leads to the condition called NeuroAIDS. Yan Zhang leads a team of Med Chem faculty and pharmacologists that is working to understand the mechanism of the disease as well as to discover and design novel and effective treatments for this devastating condition. The figure shows a putative bivalent inhibitor designed to prevent viral invasion triggered by formation of the μ-opioid receptor – CCR5 (which has been associated with the HIV-1 virus) heterodimer.

Anti-HIV therapeutics

Behavioral Effects of Drugs

The investigation of behaviorally active drugs draws on a number of disciplines: psychology, pharmacology, chemistry, psychiatry, biochemistry, anatomy and physiology. Research in this area includes the investigation of drug-behavior-neurochemical interactions (neuropsychopharmacology) and drug-behavior interactions (behavioral pharmacology). Such studies include relationships between chemical structure and behavioral activity (SAR) and mechanisms of action. Behavioral effects of drugs have played key roles in drug discovery and development of many different types of drugs that exert their effects on the CNS, including anesthetics, anti-drugs (-anxiety, -convulsants, -emetics, -Parkinson’s, -dementia, -psychotic), CNS stimulants, hallucinogens and analgesics. VCU medicinal chemists Richard Glennon and Malgorzata Dukat in collaboration with members of VCU Pharmacology and Toxicology have pioneered several key pharmacological assays and, in particular, are noted for the Drug Discrimination paradigm wherein the subjective effect of drugs in nonhuman animals or humans is evaluated. For example, a rodent can be “trained” to recognize a particular psychoactive drug, and when presented with another molecule, that animal can report whether that new compound provides the same behavioral effect as the training drug. The Department’s Richard Young is an internationally recognized expert on drug discrimination.

Behavioral Effects of Drugs

Bioinformatics

Bioinformatics techniques are now routinely used to identify disease- and non-disease-related genes, quantify the variability within and between genes and gene families, and even characterize entire genomes. Combining this data with structural information about the corresponding proteins, their families and associated functions can lead to the discovery of a therapeutically relevant protein, shed light on the mechanism of action of a class of proteins, or provide key insights for the design and development of small-molecule therapeutic agents. VCU Medicinal Chemistry faculty members are harnessing the power of bioinformatics, with a current focus on the development of new antibiotics. Utilizing their knowledge of metabolic networks and essential genes, Glen Kellogg and Yan Zhang, in collaboration with a faculty member in the VCU School of Dentistry, have designed inhibitors for a “druggable” essential target, meso-diaminopimelate dehydrogenase, which is found in Porphyromonas gingivalis-like species found in the oral microbiome. Philip Mosier and Colleagues at the VCU Center for the Study of Biological Complexity is actively engaged in a translational research project to assign structure and function to genes identified in the genomes of lytic bacteriophages (viruses that infect and destroy bacteria) like B. anthracis (anthrax). Aaron May is investigating the use of genome-wide random mutagenesis combined with bacterial genome sequencing to identify molecular targets of the bacterial Type III Secretion System, an apparatus used by Gram-negative bacteria to cause infection.

Bioinformatics-1

Centrally-acting Agents

Communication within the brain occurs through specialized cells termed neurons, and is typically chemical using substances called “neurotransmitters”. Neuropsychiatric disorders are believed to be associated with an imbalance of neurotransmitters like serotonin, norepinephrine, dopamine or acetylcholine in the extracellular space, i.e., synapses. Central acting agents are molecules that play an important role in homeostasis; they can be agonists and/or antagonists and can increase or decrease synaptic concentrations of neurotransmitters. According to the World Health Organization, neuropsychiatric disorders (mental, behavioral or neurological disorders), which are diseases of the central nervous system (CNS), are the leading cause of disability in the US. VCU medicinal chemists have an international reputation from our research in CNS. Our xenobiotic research – with emphases on novel chemotypes and mechanisms of action – in Alzheimer’s disease (Shijun Zhang), depression (Richard Glennon and Malgorzata Dukat), drugs of abuse (Glennon and Yan Zhang), schizophrenia (Glennon) and pain treatment (Y. Zhang) is a major strength of the department. This work stresses an understanding – structural, pharmacological and chemical – of receptors and transporters, many of which are membrane-bound. Drug discovery efforts are to design and utilize subtype-selective orthosteric and allosteric ligands as molecular probes that reveal minute details of receptor and transporter action. This research is highly multidisciplinary, involving: classical drug design (Glennon, Dukat, Y. Zhang and S. Zhang), computational medicinal chemistry (Y. Zhang, Dukat, Philip Mosier and Glen Kellogg), structural biology of membrane-bound proteins (Youzhong Guo), in vitro and in vivo assays, animal behavioral studies (Dukat and Richard Young), and extensive collaborations with the VCU Department of Pharmacology and Toxicology, which is among the top ten pharmacology departments for CNS research.

Centrally-acting Agents

Chemical Biology

Chemical Biology is the use of chemical techniques and tools to study biological systems. Chemical biology research works to develop an understanding of potential drug targets at the molecular level in cellular environments and apply that knowledge to the discover of early stage inhibitors for drug development. Chemical biology techniques and tools can be used in all therapeutic areas and can be very powerful when combined with structural biology. Keith Ellis leads a team working on the chemical biology of several kinases, including those involved in cancer and endocrine disorders. Aaron May is using chemical biology techniques to investigate new molecular targets for use in treating bacterial and other infectious diseases. Umesh Desai’s research team is at the forefront of applying chemical biology principles and methods to the investigations of glycosaminoglycans (GAGs) and other sugar-based biological molecules.

Chemical Biology

Drugs of Abuse

Why investigate drugs of abuse? Certainly one reason might be to find a “cure” for drug addiction. However, perhaps surprisingly, much of what we currently know concerning certain neurotransmitter receptors and transporters derives from studies with drugs of abuse such as, for example, central stimulants like cocaine, hallucinogens like LSD, opioids, cannabinoids like Δ9-THC in marijuana, and what are called “designer drugs” like in “spice” or “bath salts”. Furthermore, an appreciation of these agents and their associated mechanisms of action has directly or indirectly led to novel treatments for, or to a better understanding of, for example, psychoses, depression, pain, appetite control, and other disorders, and to the development of chemical “tools” for radioligand binding and imaging studies. Perhaps basic to the above is elucidation of the structure-activity relationships (called SAR) and mechanisms of action of the hundreds of currently abused substances. Synthetic chemistry, homology modeling/docking, SAR and QSAR (quantitative structure-activity relationship) studies, as well as many different pharmacological assays (e.g., receptor binding, electrophysiology, transporter function, in vivo behavioral effects of drugs in animal studies, and etc.) are being conducted. VCU medicinal chemist Richard Glennon was at the forefront of research that illuminated the roles of the various subtypes of serotonin receptors, which gained some of their prominence and notoriety from being the target for LSD. Glennon’s lab is currently exploring the designer drug components of bath salts, one of which is similar to cathinone, an amphetamine-like stimulant, found in the khat plant of Africa and the Arabian Peninsula. Yan Zhang has been researching approaches to optimize the subtype selectivity of opioid-binding ligands, which could lead to treatments for opioid addiction by blocking receptors without producing a “high”.

Drugs of Abuse

Molecular Modeling, Drug Discovery and Design

Simply, molecular modeling is a suite of computer techniques that enable visualization of molecules and their electronic, physical and chemical properties. In medicinal chemistry the focus is mostly on using these techniques to identify new active molecular entities that can be used as chemotherapeutic treatments for disease. The differences between drug discovery and drug design are mainly related to the stage of the project. In the early stages, the emphasis is on “discovering” new molecules with unique chemotypes and properties that could potentially be viewed as lead compounds. Later, as a lead is optimized for efficacy and physicochemical properties, the process becomes “design” wherein hypotheses are created from the SAR (structure-activity relationships) of a set of (sometimes) closely related analogues, and then tested by synthesizing and testing molecules that test those hypotheses. Molecular modeling research has been a keystone of the VCU Medicinal Chemistry Department for many years. Lemont Kier and Richard Glennon were early adopters of molecular orbital calculations to understand the electronic structure of drug molecules. Glen Kellogg and Donald Abraham invented the HINT (Hydropathic INTeractions) computational model to probe the hydrophobic effect and related phenomena involving water. VCU Medicinal Chemistry is very well equipped with hardware (graphics workstations and a GPU cluster) and multiple software packages encompassing the range of techniques: model building, homology modeling, docking and scoring, molecular dynamics and QSAR. Of equal note are the Department’s applications of state-of-the-art molecular modeling to significant therapeutic problems such as those related to neurochemistry (Glennon, Malgorzata Dukat, Yan ZhangShijun Zhang and Philip Mosier), enzyme inhibition (Martin Safo and Kellogg), proteins involved in coagulation, emphysema, inflammation, cystic fibrosis (Umesh Desai and Mosier) and cancer (Kellogg, Yan Zhang, Desai and Keith Ellis). 

Molecular Modeling, Drug Discovery and Design gif

Natural Product Synthesis

Natural products are secondary metabolites created by organisms in nature, often for purposes beneficial to their health and survival. The diverse structures of these molecules are often quite complex and their so-called “total synthesis” is correspondingly challenging. The use of natural products as natural products forms the bases for most of the known antibiotics classes, many anticancer and antiviral drugs, and even blockbusters such as the cholesterol lowering agent simvastatin. Natural products also include some of the most abused drugs. Yan Zhang and Keith Ellis have designed and synthesized analogues of natural products as potential therapeutics using traditional (total synthesis-based) medicinal chemistry approaches. The laboratory of Aaron May is interested in optimizing the activity of natural products with engineered biosynthesis to produce new and more potent biological effects, particularly with respect to new antibiotics.

Natural Product Synthesis

Neurodegenerative and Inflammatory Disorders

Neurodegenerative disorders are a family of diseases that are characterized by the loss of nerve structure and functions, ultimately leading to loss of cognitive functions such as memory and decision-making. This family includes Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD), Lou Gehrig's disease (Amyotrophic lateral sclerosis, ALS) and multiple sclerosis (MS). Although the exact mechanisms underlying these diseases are not yet completely understood, it is now widely accepted that multiple risk factors, including genetic, environmental, and endogenous factors, contribute to development of these complex central nervous system (CNS) disorders following a complicated network of pathways. Currently available treatments for most neurodegenerative disorders can only provide symptomatic relief and there are no cures or preventive agents. Shijun Zhang and his multidisciplinary team of medicinal chemists, molecular biologists, immunologists and pharmacologists are working at the interface between chemistry and biology to design and develop small molecules that are chemical probes and potential disease modifying agents. Ultimately, understanding the molecular mechanisms of these devastating disorders will lead to safe and effective treatments that target various risk factors such as protein aggregation, inflammation and mitochondria dysfunction

Neurodegenerative and inflammatory disorders

Next Generation Antibiotics

The widespread use of antibiotics has led to the evolution and proliferation of many pathogens that are now multidrug resistant. With an eye to the future, the VCU laboratory of Aaron May is interested in next-generation antibacterial strategies that specifically target the ability of pathogens to cause infection. Doing so allows the host immune system to clear the pathogen, and significantly lowers the chances of resistance being formed to the inhibitors. These studies are focused on naturally occurring pathogenesis inhibitors, including guadinomine B and aurodox, which are both biosynthesized by Streptomyces. Other modern approaches to antibiotic drug discovery in used by VCU Medicinal Chemistry faculty include Bioinformatics and Molecular Modeling and Drug Design.

Next-Generation Antibiotics image 1

Structural Biology

Fundamental to medicinal chemistry is the concept of structure. The structure of small molecules is the core of organic chemistry, while for medicinal chemists thje goal is to exploit those structures to elicit biological response. Especially significant is structural information regarding the biomacromolecular target for the small molecule, which then allows rational drug discovery and/or design. The VCU medicinal chemists that are members of the Institute for Structural Biology, Drug Discovery and Design (ISB3D) are experts in obtaining and exploiting these structures through the various tools of Structural Biology. We use a comprehensive array of modern biophysical, biochemical and computational techniques, but in particular we have the state-of-the-art in X-ray crystallography, a highly capable high-field NMR and access to some of the most advanced single particle cryo-electron microscopes on the US East coast. Martin Safo has led studies on several biologically important proteins, some of which have led to the development of compounds currently under trial for sickle cell disease. Youzhong Guo’s laboratory is focused on membrane protein structural biology, i.e., to decipher the structures and functions of this ubiquitous but difficult to study class of proteins and complexes at the atomic-level. His lab is also at the forefront of methods development for structural biology, including a very new efficient and economical lipidic cubic phase system for crystallization and a nanoparticles system for cryo-EM. One aspect of Glen Kellogg’s research is in implementing new computational tools that produce more accurate molecular models from less than ideal experimental structural data.

Structural Biology

QSAR Technology Development

Quantitative Structure-Activity Relationships is the keystone of computational medicinal chemistry. Simply put, the invention of QSAR linked molecular structure to biological activity with mathematics and statistics. VCU Medicinal Chemistry is internationally known for our contributions to the development of QSAR technology that have spanned more than forty years: from Lemont Kier and his topological and graph theory structure descriptors κ, χ and the E-state, to Richard Glennon and his innovative uses of Q/SAR in drug design, to Glen Kellogg and his additions to the understanding of three-dimensional QSAR fields and applications as well as the HINT program, and Umesh Desai and Philip Mosier who have extended a number of QSAR concepts to sulfated sugar polymers.

QSAR Technology Development-1

X-Ray Crystallography

X-ray crystallography has been key to our understanding of the relationship between protein structure and physiological function, and in recent years has been the driving force for structure-based drug discovery. Medicinal chemists play a key role in these efforts by applying principles of drug design to discover ligands, inhibitors or probes for experimental 3D biomacromolecular structures. Both Martin Safo and Youzhong Guo are medicinal chemists that specialize in X-ray crystallography. Both are also members of the ISB3D, which has for the past 20 years been the center for crystallographic studies at VCU and for the nearby University of Richmond. An exciting development is the installation of a new (2017!) state-of-the-art X-ray diffraction system (MicroMax-007HF generator, VariMax-HF Arc Optics, Hybrid Photon Counter, Eiger R 4M Detector, AFC11 Goniometer and Oxford Cobra Cryo-system) that provides VCU researchers with essential internal capabilities for the determination of structures. The X-ray facility is used by investigators from multiple departments in various diverse research programs such as cancer, infectious diseases, thrombosis/hemostasis, gene regulation, drug abuse and addiction, hemoglobinopathies, cardiovascular disease, systems biology, protein function and regulation, etc., many of which involve collaborations with VCU medicinal chemists. Structure-based drug discovery is a major focus for much of this research and has resulted in several preclinical and clinical drugs over the years.

X-ray Crystallography