SUPERGEN INC
S-3, 2000-12-20
PHARMACEUTICAL PREPARATIONS
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   AS FILED WITH THE SECURITIES AND EXCHANGE COMMISSION ON DECEMBER 20, 2000
                                                     REGISTRATION NO. 333-
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                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                           --------------------------

                                    FORM S-3
                             REGISTRATION STATEMENT
                                     UNDER
                           THE SECURITIES ACT OF 1933
                           --------------------------

                                 SUPERGEN, INC.
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)
                           --------------------------

<TABLE>
<S>                                 <C>                                 <C>
             DELAWARE                              2834                             91-1841574
 (State or other jurisdiction of       (Primary Standard Industrial               (IRS Employer
  incorporation or organization)       Classification Code Number)            Identification Number)
</TABLE>

                          4140 DUBLIN BLVD., SUITE 200
                            DUBLIN, CALIFORNIA 94568
                                 (925) 560-0100
  (Address, including zip code, and telephone number, including area code, of
                   Registrant's principal executive offices)
                           --------------------------

                            JOSEPH RUBINFELD, PH.D.
                     PRESIDENT AND CHIEF EXECUTIVE OFFICER
                                 SUPERGEN, INC.
                          4140 DUBLIN BLVD., SUITE 200
                            DUBLIN, CALIFORNIA 94568
                                 (925) 560-0100
 (Name, address, including zip code, and telephone number, including area code,
                             of agent for service)
                           --------------------------

                                   COPIES TO:
                               JOHN V. ROOS, ESQ.
                        WILSON SONSINI GOODRICH & ROSATI
                            PROFESSIONAL CORPORATION
                               650 PAGE MILL ROAD
                            PALO ALTO, CA 94304-1050
                                 (650) 493-9300
                           --------------------------

        APPROXIMATE DATE OF COMMENCEMENT OF PROPOSED SALE TO THE PUBLIC:
   FROM TIME TO TIME AFTER THE EFFECTIVE DATE OF THIS REGISTRATION STATEMENT.

    If the only securities being registered on this Form are being offered
pursuant to dividend or interest reinvestment plans, check the following
box. / /

    If any of the securities being registered on this Form are to be offered on
a delayed or continuous basis pursuant to Rule 415 under the Securities Act of
1933, other than securities offered only in connection with dividend or interest
reinvestment plans, check the following box. /X/

    If this Form is filed to register additional securities for an offering
pursuant to Rule 462(b) under the Securities Act, please check the following box
and list the Securities Act registration statement number of the earlier
effective registration statement for the same offering. / /

    If this Form is a post-effective amendment filed pursuant to Rule 462(c)
under the Securities Act, check the following box and list the Securities Act
registration statement number of the earlier effective statement for the same
offering. / /

    If delivery of the prospectus is expected to be made pursuant to Rule 434,
please check the following box. / /

                        CALCULATION OF REGISTRATION FEE

<TABLE>
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                                                        PROPOSED MAXIMUM     PROPOSED MAXIMUM
       TITLE OF EACH CLASS            AMOUNT TO BE     OFFERING PRICE PER   AGGREGATE OFFERING        AMOUNT OF
  OF SECURITIES TO BE REGISTERED      REGISTERED(1)         SHARE(2)            PRICE(1)(2)      REGISTRATION FEE(3)
--------------------------------------------------------------------------------------------------------------------
<S>                                 <C>                <C>                  <C>                  <C>
Common Stock $0.001 par value.....       697,533            $19.53125           $13,623,691           $3,596.65
--------------------------------------------------------------------------------------------------------------------
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</TABLE>

(1) Pursuant to Rule 416 under the Securities Act, this Registration Statement
    also relates to a presumably indeterminable number of shares of Common Stock
    which are issuable upon stock splits, stock dividends, recapitalizations or
    other similar transactions.

(2) Estimated solely for the purpose of computing the registration fee and based
    on the average high and low sale prices of the Common Stock of
    SuperGen, Inc. as reported on the Nasdaq National Market on December 15,
    2000.

(3) Computed pursuant to Rule 457(c) based on the average high and low sale
    prices of the Common Stock of SuperGen, Inc. as reported on the Nasdaq
    National Market on December 15, 2000.

    THE REGISTRANT HEREBY AMENDS THIS REGISTRATION STATEMENT ON SUCH DATE OR
DATES AS MAY BE NECESSARY TO DELAY ITS EFFECTIVE DATE UNTIL THE REGISTRANT SHALL
FILE A FURTHER AMENDMENT WHICH SPECIFICALLY STATES THAT THIS REGISTRATION
STATEMENT SHALL THEREAFTER BECOME EFFECTIVE IN ACCORDANCE WITH SECTION 8(a) OF
THE SECURITIES ACT OR UNTIL THE REGISTRATION STATEMENT SHALL BECOME EFFECTIVE ON
SUCH DATE AS THE COMMISSION, ACTING PURSUANT TO SAID SECTION 8(a), MAY
DETERMINE.

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<PAGE>
                                   PROSPECTUS

                               ------------------

                            DATED DECEMBER 20, 2000

                                 697,533 SHARES

                                 SUPERGEN, INC.

                                  COMMON STOCK

                               ------------------

    The selling stockholders of SuperGen, Inc. ("SuperGen," "we," or "the
Company") listed on page 16 may offer and resell up to 697,533 shares of
SuperGen, Inc. common stock under this Prospectus, for their own account. We
will not receive any proceeds from such sales. We issued these shares of our
common stock to the selling stockholders in private transactions.

    Our common stock is listed on the Nasdaq National Market under the symbol
"SUPG". On December 19, 2000, the last reported sale price for the Common Stock
on the Nasdaq National Market was $19.25 per share.

    SEE "RISK FACTORS" BEGINNING AT PAGE 4 TO READ ABOUT CERTAIN FACTORS YOU
SHOULD CONSIDER BEFORE BUYING SHARES OF THE COMMON STOCK.

                             ---------------------

    NEITHER THE SECURITIES AND EXCHANGE COMMISSION NOR ANY SECURITIES COMMISSION
HAS APPROVED OR DISAPPROVED OF THESE SECURITIES OR PASSED UPON THE ACCURACY OR
ADEQUACY OF THIS PROSPECTUS. ANY REPRESENTATION TO THE CONTRARY IS A CRIMINAL
OFFENSE.

               The date of this Prospectus is December 20, 2000.
<PAGE>
                                    SUMMARY

    We are an emerging pharmaceutical company dedicated to the acquisition,
rapid development and commercialization of oncology therapies for solid tumors
and hematological malignancies. We seek to minimize the time, expense and
technical risk associated with drug commercialization by identifying and
acquiring pharmaceutical compounds in the later stages of development, rather
than committing significant resources to the research phase of drug discovery.
We intend to retain significant participation in the commercialization of our
proprietary products by funding and undertaking human clinical development
ourselves. We believe this will allow us to maximize the commercial value of our
products by either directly marketing our products or licensing them on more
favorable terms than would be available if licensed earlier in the development
cycle.

    Our lead product candidate is rubitecan, an oral chemotherapy compound in
the camptothecin class which is in pivotal Phase III clinical trials for
pancreatic cancer, the fourth leading cause of death by cancer in the United
States. Results of Phase II clinical trials conducted using rubitecan for
treatment of pancreatic cancer indicate a favorable comparison with historical
treatment options in terms of quality of life, survival data and tumor size
reduction. Rubitecan is a second-generation topoisomerase I inhibitor that
causes single-strand breaks in the DNA of rapidly dividing tumor cells. We
believe that rubitecan may have significant advantages over many existing
anticancer drugs. These advantages include increased survival, oral dosing and a
superior side effect profile. We believe that rubitecan is a platform drug for
leadership in the treatment of a broad array of solid tumors and hematological
malignancies.

    We are evaluating rubitecan in three separate stand-alone pivotal Phase III
clinical trials for pancreatic cancer. One 400-patient Phase III clinical trial
is evaluating the efficacy of rubitecan as second-line therapy for those
patients having previously failed treatment with gemcitabine, or
Gemzar-Registered Trademark-. A second 400-patient Phase III clinical trial is
evaluating the efficacy of rubitecan as salvage therapy for those patients
having previously failed multiple treatment regimens. The third 1,000-patient
Phase III clinical trial is evaluating rubitecan's efficacy as first-line
therapy in comparison with Gemzar. The trials are randomized, unblinded studies
being conducted in approximately 200 centers with survival as the primary
endpoint. We commenced these trials in November 1998 and we have enrolled over
1,500 patients in the aggregate. If any one of these trials is successful, we
anticipate filing a New Drug Application, or NDA, with the U.S. Food and Drug
Administration, or FDA. Current enrollment projections indicate a completion of
patient accrual for the second-line trial in the fourth quarter of 2000, which
with positive data could lead to a filing of an NDA with the FDA by mid-2001.

    We are aggressively pursuing additional clinical trials using rubitecan both
as a single therapeutic agent and in combination with other anticancer agents in
both solid tumors and hematological malignancies. We intend to make available to
physicians copies of peer-reviewed medical journal articles and other validated
scientific information related to these trials. We believe this will provide
physicians with more up-to-date product information and will better enable them
to meet their patients' medical needs.

    We entered into an alliance with Abbott Laboratories under which Abbott will
market and distribute rubitecan and invest in shares of our common stock. We
will co-promote rubitecan with Abbott in the United States and Abbott has
exclusive rights to market rubitecan outside of the United States. In the U.S.
market, we will share profits from product sales equally with Abbott. Outside
the U.S. market, Abbott will pay us royalties and transfer fees based on product
sales. We will remain responsible for pursuing and funding the clinical
development of rubitecan and obtaining regulatory approval for the product in
the United States, Canada and the member states of the European Union.

    We will receive a number of equity investments and cash payments from Abbott
which, when aggregated, amount to approximately $150 million. Each equity
investment and cash payment is conditioned upon the achievement of certain
developmental and sales milestones. In addition, we

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granted Abbott an option to purchase up to 49% of the outstanding shares of our
common stock at an exercise price of $85 per share which expires in March 2003.

    We are also pursuing the clinical development of
Nipent-Registered Trademark- and decitabine for the treatment of certain solid
tumor cancers and hematological disorders. We acquired Nipent from
Warner-Lambert Company in 1996 and we are selling this drug in the United States
for the treatment of hairy cell leukemia, a type of B-lymphocytic leukemia. We
believe that Nipent has a unique mechanism of action and Phase II trials
indicate that it may have activity in a variety of other hematologic cancers. In
oncology, we are pursuing treatments for lymphatic malignancies and disorders.
In addition, Nipent has shown activity in various autoimmune diseases, including
graft-versus-host disease which is not responsive to standard therapies, and
rheumatoid arthritis. We estimate the United States markets for both
graft-versus-host disease and rheumatoid arthritis are larger than the market
for Nipent's leukemia applications. We intend to initiate pivotal trials with
Nipent in graft-versus-host disease in the next few months.

    Decitabine has been successful in multiple Phase II trials in the United
States and Europe for treating myelodysplastic syndromes, or MDS, chronic
myeloid leukemia and acute myeloid leukemia. Based on positive results from
these studies, we are initiating a randomized Phase III study comparing
decitabine to best supportive care for MDS. We expect to commence patient
enrollment within the next few months. In addition, preliminary results suggest
that decitabine has activity in solid tumors such as non-small cell lung cancer
and in sickle cell anemia. We are currently exploring strategies for pivotal
studies for decitabine in sickle cell anemia.

    In July 2000, we finalized an agreement with AVI BioPharma, Inc., or AVI, to
obtain the U.S. marketing rights for Avicine-TM-, their therapeutic vaccine for
colorectal cancer. AVI has informed us that they intend to initiate a Phase III
clinical trial with Avicine within the next few months. We will share U.S.
developmental and regulatory approval costs for Avicine and upon
commercialization in the U.S. we will split all U.S. profits. AVI and SuperGen
will jointly determine the optimum development strategy for the international
marketplace and will share all profits received. In addition to an up front
equity investment, we are obligated to make additional payments to AVI based on
successful achievement of developmental, regulatory approval, and
commercialization milestones over the next several years. As part of this
agreement, we obtained the right of first discussion to all of AVI's oncology
compounds and an option to acquire an additional 10% of AVI's common stock.

    We incorporated in March 1991 as a California corporation and changed our
state of incorporation to Delaware in November 1997. Our executive offices are
located at 4140 Dublin Blvd., Suite 200, Dublin, California 94568, and our
telephone number at that address is (925) 560-0100. We maintain a website on the
internet at WWW.SUPERGEN.COM. Our website, and the information contained
therein, is not a part of this prospectus.

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                                  RISK FACTORS

    YOU SHOULD CAREFULLY CONSIDER THE RISKS DESCRIBED BELOW, TOGETHER WITH ALL
OF THE OTHER INFORMATION INCLUDED IN OR INCORPORATED BY REFERENCE INTO THIS
PROSPECTUS, BEFORE MAKING AN INVESTMENT DECISION. THE RISKS AND UNCERTAINTIES
DESCRIBED BELOW ARE NOT THE ONLY ONES WE FACE. IF ANY OF THE FOLLOWING RISKS
ACTUALLY OCCUR, OUR BUSINESS COULD BE HARMED. IN SUCH CASE, THE TRADING PRICE OF
OUR COMMON STOCK COULD DECLINE, AND YOU MAY LOSE ALL OR PART OF YOUR INVESTMENT.

IF THE RESULTS OF FURTHER CLINICAL TESTING INDICATE THAT OUR PROPOSED PRODUCTS
ARE NOT SAFE AND EFFECTIVE FOR HUMAN USE, OUR BUSINESS WILL SUFFER.

    Most of our products are in the development stage and prior to their sale
will require the commitment of substantial resources. All of the potential
proprietary products that we are currently developing will require extensive
pre-clinical and clinical testing before we can submit any application for
regulatory approval. Before obtaining regulatory approvals for the commercial
sale of any of our products, we must demonstrate through pre-clinical testing
and clinical trials that our product candidates are safe and effective in
humans. Conducting clinical trials is a lengthy, expensive and uncertain
process. Completion of clinical trials may take several years or more. The
length of time generally varies substantially according to the type, complexity,
novelty and intended use of the product candidate. Our clinical trials may be
suspended at any time if we or the FDA believe the patients participating in our
studies are exposed to unacceptable health risks. We may encounter problems in
our studies which will cause us or the FDA to delay or suspend the studies. Our
commencement and rate of completion of clinical trials may be delayed by many
factors, including:

    - ineffectiveness of the study compound, or perceptions by physicians that
      the compound is not effective for a particular indication;

    - inability to manufacture sufficient quantities of compounds for use in
      clinical trials;

    - failure of the FDA to approve our clinical trial protocols;

    - failure of our contract research organization to devote sufficient time
      and resources to our studies or to comply with strictly enforced Good
      Clinical Practice, or GCP standards;

    - slower than expected rate of patient recruitment;

    - inability to adequately follow patients after treatment;

    - unforeseen safety issues;

    - lack of efficacy during the clinical trials; or

    - government or regulatory delays.

    The clinical results we have obtained to date do not necessarily predict
that the results of further testing, including later-stage controlled human
clinical testing, will be successful. If our trials are not successful, or are
perceived as not successful by the FDA or physicians, our business, financial
condition and results of operations will be harmed.

IF WE FAIL TO OBTAIN REGULATORY MARKETING APPROVALS IN A TIMELY MANNER, OUR
BUSINESS WILL SUFFER.

    Even if we believe our trials are successful, the FDA may require additional
clinical testing and, therefore we would have to commit additional unanticipated
resources. The FDA has substantial discretion in the drug approval process. We
cannot assure you that we will obtain the necessary regulatory approvals to
market our products. The FDA and comparable agencies in foreign countries impose
substantial requirements for the introduction of both new pharmaceutical
products and generic products through lengthy and detailed clinical testing
procedures, sampling activities and other costly

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and time-consuming compliance procedures. We have not yet received marketing
approval for any of our internally developed proprietary products. Our
proprietary drugs and products will require lengthy clinical trials along with
FDA and comparable foreign agency review as new drugs. Our generic drugs will
also require regulatory review and approval.

    We cannot predict with certainty if or when we might submit for regulatory
review those products currently under development. Once we submit our potential
products for review, we cannot assure you that the FDA or other regulatory
agencies will grant approvals for any of our pharmaceutical products on a timely
basis or at all. Sales of our products outside the United States will be subject
to regulatory requirements governing clinical trials and marketing approval.
These requirements vary widely from country to country and could delay the
introduction of our products in those countries.

IF OUR RELATIONSHIP WITH ABBOTT IS NOT SUCCESSFUL, OUR BUSINESS COULD BE HARMED.

    Our strategic relationship with Abbott is important to our success. However,
that relationship may not be successful. We cannot assure you that we will
receive any additional payments from Abbott or that the relationship will be
commercially successful. The transactions contemplated by our agreements with
Abbott, including the equity purchases and cash payments, are subject to
numerous risks and conditions. For example:

    - we may fail to achieve clinical and sales milestones;

    - the contract research organization performing some of the clinical
      research services for our rubitecan development program may fail to
      perform its obligations under our agreements harming our clinical approval
      activities;

    - rubitecan may fail to achieve regulatory approval domestically and
      internationally;

    - rubitecan may not be commercially successful;

    - Abbott may fail to perform its obligations under our agreements, such as
      failing to devote sufficient resources to marketing rubitecan; and

    - our agreements with Abbott may be terminated in their entirety or on a
      territory-by-territory basis against our will.

    The occurrence of any of these events could severely harm our business.

WE HAVE GRANTED CERTAIN RIGHTS TO ABBOTT THAT COULD NEGATIVELY AFFECT YOUR
INVESTMENT.

    We have granted Abbott an option to purchase shares of our common stock so
that upon its exercise Abbott will own up to 49% of our outstanding common
stock. Our ability to satisfy this contractual obligation is subject to a number
of conditions outside of our control, including:

    - stockholder approval of a potential change in control under the rules of
      the Nasdaq National Market; and

    - clearance of the purchase by federal antitrust regulators.

    If we do not satisfy any of these conditions, Abbott could terminate our
relationship. If we obtain all necessary approvals and Abbott exercises its
option, the stock ownership of our other stockholders will be diluted and Abbott
will have significant influence over us. Abbott's right to exercise this option,
and Abbott's share ownership after exercise, may discourage other parties from
acquiring us.

    Abbott has a right of first discussion with respect to our product portfolio
and a right of first refusal to acquire us. These rights may discourage third
parties from bidding on any assets that we wish to sell or license and may
discourage acquisition bids. These provisions may limit the price that investors
might be willing to pay in the future for shares of our common stock.

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WE HAVE A HISTORY OF OPERATING LOSSES AND AN ACCUMULATED DEFICIT, WE MAY NOT
ACHIEVE OR MAINTAIN PROFITABILITY IN THE FUTURE, AND WE MAY NEED TO OBTAIN
ADDITIONAL FUNDING.

    We incurred cumulative losses of $118.2 million for the period from
inception through September 30, 2000. Currently we are not profitable and we
expect to continue to incur substantial operating losses at least through 2001.
Our ability to achieve profitability will depend primarily on our ability to
obtain regulatory approval for and successfully commercialize rubitecan. Our
success will also depend, to a lesser extent, on our ability to develop and
obtain regulatory approval of Nipent for indications other than hairy cell
leukemia and to bring our proprietary products to market. Our ability to become
profitable will also depend upon a variety of other factors, including the
following:

    - increases in the level of our research and development, including the
      timing and costs to complete or expand our clinical trials;

    - regulatory approvals of competing products, or expanded labeling approvals
      of existing products;

    - increases in sales and marketing expenses related to the commercial launch
      of rubitecan;

    - delays in or inadequate commercial sales of rubitecan, once regulatory
      approvals have been received; and

    - expenditures associated with acquiring products, technologies or companies
      and further developing these assets.

    We cannot predict the outcome of these factors and we cannot assure you that
we will ever become profitable.

    Even if we do become profitable, we may need substantial additional funding.
We expect that our rate of spending will accelerate as a result of increased
clinical trial costs and expenses associated with regulatory approval and
commercialization of our products now in development. We anticipate that our
capital resources will be adequate to fund operations and capital expenditures
at least through 2002. However, if we experience unanticipated cash requirements
during this period, we could require additional funds much sooner. Our business,
results of operations and cash flows will be adversely affected if we fail to
obtain adequate funding in a timely manner, or at all. We may receive funds from
the sale of equity securities, or the exercise of outstanding warrants and stock
options. Additionally, we may receive funds upon the achievement of certain
developmental and sales milestones pursuant to our agreement with Abbott.
However, we cannot assure you that any of those fundings will occur, or if they
occur, that they will be on terms favorable to us. Also, the dilutive effect of
those fundings could adversely affect our results per share.

WE HAVE LIMITED SALES AND MARKETING CAPABILITIES AND NO DISTRIBUTION
CAPABILITIES AND MAY NOT BE ABLE TO SUCCESSFULLY COMMERCIALIZE OUR PRODUCTS.

    We currently have limited sales and marketing resources and no distribution
capability. Although we have 22 sales and marketing personnel focusing on the
sale of our products to hospitals and hospital buying groups, we anticipate
relying on third parties to sell and market some of our primary products. For
instance, we will co-promote the potential sale of rubitecan with Abbott.
However, we may not be able to enter into additional sales and marketing
arrangements with others on acceptable terms, if at all. If our arrangements
with third parties are not successful, or if we are unable to enter into
third-party arrangements, then we may need to substantially expand our sales and
marketing force. We may not succeed in enhancing our sales and marketing
capabilities or have sufficient resources to do so. If we do develop such
capabilities, we will compete with other companies that have experienced and
well-funded sales and marketing operations. We currently rely on third parties
to distribute our products and expect to continue to do so in the future. If we
fail to establish successful sales and marketing capabilities or fail to enter
into successful marketing arrangements with third parties, or if

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our third party distributors fail to perform their obligations, our business,
financial condition and results of operations will be materially and adversely
affected.

IF WE FAIL TO COMPLY WITH THE GOVERNMENTAL REGULATIONS, OUR BUSINESS WILL
SUFFER.

    All new drugs, including our products under development, are subject to
extensive and rigorous regulation by the FDA, and comparable agencies in state
and local jurisdictions and in foreign countries. These regulations govern,
among other things, the development, testing, manufacturing, labeling, storage,
pre-market approval, advertising, promotion, sale and distribution of our
products. Satisfaction of these requirements typically takes several years and
the time needed to satisfy them may vary substantially, based on the type,
complexity and novelty of the pharmaceutical product. The effect of government
regulation may be to delay or to prevent marketing of our potential products for
a considerable period of time and to impose costly procedures upon our
activities. If regulatory approval of our products is granted, such approval may
impose limitations on the indicated uses for which our products may be marketed.
Further, even if regulatory approval is obtained for a product, later discovery
of previously unknown problems may result in restrictions of the product,
including withdrawal of the product from the market.

    Among the conditions for FDA approval of all of our products in development
is the requirement that the manufacturer's (at either our facilities or those of
a third party manufacturer) quality control and manufacturing procedures conform
to current Good Manufacturing Practices, or GMPs, which must be followed at all
times. The FDA and foreign regulatory authorities strictly enforce GMP
requirements through periodic unannounced inspections. We cannot assure you that
the FDA will determine that our facilities and manufacturing procedures or any
third party manufacturer of our products will conform to GMP requirements.
Additionally, we, or our third party manufacturer, must pass a pre-approval
inspection before we can obtain marketing approval for any of our products in
development. Failure to comply with applicable FDA and other regulatory
requirements can result in sanctions being imposed on us or the manufacturers of
our products including warning letters, product recalls or seizures,
injunctions, refusals to permit products to be imported into or exported out of
the United States, refusals of the FDA to grant pre-market approval or to allow
us to enter into government supply contracts, withdrawals of previously approved
marketing applications, civil fines and criminal prosecutions.

    We and our contract research organizations are also required to comply with
current GCP regulations and guidelines enforced by the FDA for all of our
products in clinical development. FDA enforced GCPs through periodic inspections
of study sponsors, principal investigators, and study sites. If we or our
contract research organizations fail to comply with applicable GCPs, the
clinical data generated in our studies may be deemed unreliable and FDA may
require us to perform additional studies before approving our marketing
applications. We cannot assure you that FDA will determine that any of our
studies for products in clinical development comply with GCPs.

    The FDA's policies may change and additional government regulations may be
promulgated which could prevent or delay regulatory approval of our products. We
cannot predict the likelihood of adverse governmental regulation which may arise
from future legislative or administrative action, either in the United States or
abroad.

IF WE FAIL TO COMPETE EFFECTIVELY, PARTICULARLY AGAINST LARGER, MORE ESTABLISHED
PHARMACEUTICAL COMPANIES WITH GREATER RESOURCES, OUR BUSINESS WILL SUFFER.

    Factors affecting competition in the pharmaceutical industry vary depending
on the extent to which the competitor is able to achieve a competitive advantage
based on proprietary technology. These factors include financial resources,
research and development capabilities, and manufacturing and marketing
experience and resources. If we are able to establish and maintain a significant
proprietary

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<PAGE>
position with respect to our proprietary products, competition will likely
depend primarily on the effectiveness of our products, their acceptance in the
marketplace and their pricing and the number, gravity and severity of their
unwanted side effects as compared to alternative products.

    Our competitors have substantially greater financial, research and
development, manufacturing and marketing experience and resources than we do and
represent substantial long-term competition for us. These competitors and
probable competitors include established companies such as Eli Lilly & Co.,

    Ortho-McNeil Pharmaceutical, Amgen Inc., Bristol-Myers Squibb Company and
Immunex Corp. If these companies succeed in developing pharmaceutical products
that are more effective or less costly than any that we may develop or market,
our business will suffer.

THE PATENTS ON THE COMPOUNDS FOR WHICH WE ARE DEVELOPING GENERIC AND EXTRA
PRODUCTS ARE HELD BY THIRD PARTIES. IF THESE PATENTS ARE EXPANDED IN SCOPE OR DO
NOT EXPIRE WHEN ANTICIPATED, OUR BUSINESS COULD SUFFER.

    We plan to develop and market several generic and Extra drugs based on
existing compounds, some of which are currently protected by one or more patents
held by others. If the existing patent protection for these drugs is maintained
or expanded, it is unlikely that we will be able to market our own generic and
Extra versions of those drugs without obtaining a license from the patent owner,
which may not be available on commercially acceptable terms, or at all.

WE DEPEND ON THIRD PARTIES FOR MANUFACTURING AND STORAGE OF OUR PRODUCTS AND OUR
BUSINESS MAY BE HARMED IF THE MANUFACTURE OF OUR PRODUCTS IS INTERRUPTED OR
DISCONTINUED.

    We have no manufacturing facilities and we currently rely on third parties
for manufacturing activities related to all of our products. As we develop new
products and increase sales of our existing products, we must establish and
maintain relationships with manufacturers to produce and package sufficient
supplies of our finished pharmaceutical products, including rubitecan.

    Our manufacturing strategy presents the following risks:

    - delays in scale-up to quantities needed for multiple clinical trials could
      delay clinical trials, regulatory submissions and commercialization of our
      products in development;

    - our current and future manufacturers are subject to ongoing periodic
      unannounced inspection by the FDA and corresponding state agencies for
      compliance with strictly enforced GMP regulations and similar foreign
      standards, and we do not have control over our third-party manufacturers'
      compliance with these regulations and standards;

    - if we need to change to other commercial manufacturing contractors, the
      FDA and comparable foreign regulators must approve these contractors prior
      to our use. This would require new testing and compliance inspections. The
      new manufacturers would have to be educated in, or themselves develop
      substantially equivalent processes necessary for, the production of our
      products. In addition, the FDA and comparable foreign regulators would
      need to approve the new manufacturers;

    - if market demand for our products increases suddenly, our current
      manufacturers might not be able to fulfill our commercial needs, which
      would require us to seek new manufacturing arrangements and may result in
      substantial delays in meeting market demand; and

    - we may not have intellectual property rights, or may have to share
      intellectual rights, to any improvements in the manufacturing processes or
      new manufacturing processes for our products.

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<PAGE>
    Any of these factors could delay clinical trials or commercialization of our
products under development, interfere with current sales, entail higher costs
and result in our being unable to effectively sell our products.

    In addition, we store the majority of the unpurified, bulk form of Nipent at
a single location. Improper storage, fire, natural disaster, theft or other
conditions at this location that may lead to the loss or destruction of the bulk
concentrate could adversely affect our business, results of operations and cash
flows.

    We do not currently intend to manufacture any pharmaceutical products,
although we may choose to do so in the future. If we decide to manufacture
products, we would be subject to the regulatory risks and requirements described
above. We will also be subject to similar risks regarding delays or difficulties
encountered in manufacturing these pharmaceutical products and we will require
additional facilities and substantial additional capital. In addition, we have
only limited experience in manufacturing pharmaceutical products. We cannot
assure you that we would be able to manufacture any of these products
successfully in accordance with regulatory requirements and in a cost-effective
manner.

ASSERTING, DEFENDING AND MAINTAINING INTELLECTUAL PROPERTY RIGHTS COULD BE
DIFFICULT AND COSTLY AND FAILURE TO DO SO WILL HARM OUR ABILITY TO COMPETE AND
THE RESULTS OF OUR OPERATIONS.

    If competitors develop substantially equivalent proprietary information and
techniques or otherwise gain access to our trade secrets, if our trade secrets
are disclosed or if we cannot effectively protect our rights to unpatented trade
secrets, our business will be harmed.

    The pharmaceutical fields are characterized by a large number of patent
filings. A substantial number of patents have already been issued to other
pharmaceutical companies, research or academic institutions or others.
Competitors may have filed applications for or have been issued patents and may
obtain additional patents and proprietary rights related to products or
processes that compete with or are similar to ours. We may not be aware of all
of the patents potentially adverse to our interests that may have been issued to
others.

    We actively seek patent protection for our proprietary products and
technologies. We have a number of United States patents and also have licenses
to, or assignments of, numerous patents issued both in the United States and
elsewhere. We may also license our patents outside the United States.
Limitations on patent protection outside the United States, and differences in
what constitutes patentable subject matter in countries outside the United
States, may limit the protection we have on patents or licenses of patents
outside the United States.

    Litigation may be necessary to protect our patent position, and we cannot be
certain that we will have the required resources to pursue the necessary
litigation or otherwise to protect our patent rights. Our efforts to protect our
patents may fail. In addition to pursuing patent protection in appropriate
cases, we also rely on trade secret protection for unpatented proprietary
technology. However, trade secrets are difficult to protect. Our trade secrets
or those of our collaborators may become known or may be independently
discovered by others.

    Our proprietary products are dependent upon compliance with numerous
licenses and agreements. These licenses and agreements require us to make
royalty and other payments, reasonably exploit the underlying technology of the
applicable patents, and comply with regulatory filings. If we fail to comply
with these licenses and agreements, we could lose the underlying rights to one
or more of these potential products, which would adversely affect our business,
results of operations and cash flows.

    From time to time we receive correspondence inviting us to license patents
from third parties. Although we know of no pending patent infringement suits,
discussions regarding possible patent infringements or threats of patent
infringement litigation either related to patents held by us or our

                                       9
<PAGE>
licensors or our products or proposed products, there has been, and we believe
that there will continue to be, significant litigation in the pharmaceutical
industry regarding patent and other intellectual property rights. Claims may be
brought against us in the future based on patents held by others. These persons
could bring legal actions against us claiming damages and seeking to enjoin
clinical testing, manufacturing and marketing of the affected product. If we
become involved in any litigation, it could consume a substantial portion of our
resources, regardless of the outcome of the litigation. If any of these actions
are successful, in addition to any potential liability for damages, we could be
required to obtain a license to continue to manufacture or market the affected
product. We cannot assure you whether we would prevail in any of these actions
or that we could obtain any licenses required under any of these patents on
acceptable terms, if at all.

IF WE LOSE KEY PERSONNEL OR ARE UNABLE TO ATTRACT AND RETAIN ADDITIONAL, HIGHLY
SKILLED PERSONNEL REQUIRED FOR THE EXPANSION OF OUR ACTIVITIES, OUR BUSINESS
WILL SUFFER.

    Our success is dependent on key personnel, including Dr. Rubinfeld, our
President and Chief Executive Officer, and members of our senior management and
scientific staff. To successfully expand our operations, we will need to attract
and retain additional, highly skilled individuals, particularly in the areas of
sales, marketing, clinical administration, manufacturing and finance. We compete
with other companies for the services of existing and potential employees. We
believe our compensation and benefits packages are competitive for our
geographical region and our industry group. However, we may be at a disadvantage
to the extent that potential employees may favor larger, more established
employers.

THE CONTINUING EFFORTS OF GOVERNMENT AND THIRD-PARTY PAYERS TO CONTAIN OR REDUCE
THE COSTS OF HEALTHCARE MAY ADVERSELY AFFECT OUR REVENUES AND PROFITABILITY.

    Our revenues and profitability may be affected by the continuing efforts of
governmental and third-party payers to contain or reduce the costs of health
care. We cannot predict the effect that these health care reforms may have on
our business, and it is possible that any of these reforms will adversely affect
our business. In addition, in both the United States and elsewhere, sales of
prescription pharmaceuticals are dependent in part on the availability of
reimbursement to the consumer from third-party payers, like government and
private insurance plans. Third-party payers are increasingly challenging the
prices charged for medical products and services. If our current and proposed
products are not considered cost-effective, reimbursement to the consumer may
not be available or be sufficient to allow us to sell products on a competitive
basis.

WE MAY BE SUBJECT TO PRODUCT LIABILITY LAWSUITS AND OUR INSURANCE MAY BE
INADEQUATE TO COVER DAMAGES.

    Clinical trials or marketing of any of our current and potential products
may expose us to liability claims from the use of these products. We currently
carry product liability insurance. However, we cannot be certain that we will be
able to maintain insurance on acceptable terms for clinical and commercial
activities or that the insurance would be sufficient to cover any potential
product liability claim or recall. If we fail to have sufficient coverage, our
business, results of operations and cash flows could be adversely affected.

IF WE ARE UNABLE TO COMPLY WITH ENVIRONMENTAL LAWS AND REGULATIONS, OUR BUSINESS
MAY BE HARMED.

    We are subject to federal, state and local laws and regulations governing
the use, manufacture, storage, handling and disposal of hazardous materials and
waste products. We currently maintain a supply of several hazardous materials at
our facilities. In the event of an accident, we could be held liable for any
damages that result, and the liability could exceed our resources. While we
currently outsource our research and development programs involving the
controlled use of biohazardous

                                       10
<PAGE>
materials, if in the future we conduct these programs, we might be required to
incur significant cost to comply with environmental laws and regulations.

ANTI-TAKEOVER PROVISIONS MAY PREVENT YOU FROM REALIZING A PREMIUM RETURN.

    Anti-takeover provisions of our certificate of incorporation and bylaws make
it more difficult for a third party to acquire us, even if doing so would be
beneficial to our stockholders. These provisions include:

    - authorization of the issuance of up to 2,000,000 shares of our preferred
      stock;

    - elimination of cumulative voting; and

    - elimination of stockholder action by written consent.

    Our bylaws establish procedures, including notice procedures, with regard to
the nomination, other than by or at the direction of our board of directors, of
candidates for election as directors or for stockholder proposals to be
submitted at stockholder meetings.

    We are also subject to Section 203 of the Delaware General Corporation Law,
an anti-takeover provision. In general, Section 203 of the Delaware General
Corporation Law prevents a stockholder owning 15% or more of a corporation's
outstanding voting stock from engaging in business combinations with a Delaware
corporation for three years following the date the stockholder acquired 15% or
more of a corporation's outstanding voting stock. This restriction is subject to
exceptions, including the approval of the board of directors and of the holders
of at least two-thirds of the outstanding shares of voting stock not owned by
the interested stockholder.

    These provisions are expected to discourage different types of coercive
takeover practices and inadequate takeover bids and to encourage persons seeking
to acquire control of our company to first negotiate with us.

    We believe that the benefits of increased protection of our potential
ability to negotiate with the proponents of unfriendly or unsolicited proposals
to acquire or restructure us outweigh the disadvantages of discouraging those
proposals because, among other things, negotiation of those proposals could
result in an improvement of their terms.

BECAUSE CURRENT OFFICERS, DIRECTORS, AND ABBOTT OWN A LARGE PERCENTAGE OF OUR
STOCK, THESE STOCKHOLDERS MAY BE ABLE TO CONTROL US AND ALSO PREVENT POTENTIALLY
BENEFICIAL ACQUISITIONS OF OUR COMPANY BY OTHERS.

    As of November 30, 2000, our officers, directors, Abbott and their
affiliates owned approximately 10.2% of the outstanding shares of our common
stock, not including stock issuable upon exercise of options or warrants. If
these stockholders were to exercise all of their options and warrants, they
would collectively own a majority of our common stock. These stockholders, if
acting together, may be able to influence the election of our directors and
other matters requiring approval by our stockholders. This concentration of
ownership may also delay or prevent a third party from acquiring us. These
stockholders may have interests that differ from our other stockholders,
particularly in the context of potentially beneficial acquisitions of our
company by others. For example, to the extent that these stockholders are our
employees, they may be less inclined to vote for acquisitions of our company by
others involving the termination of their employment or diminution of their
responsibilities or compensation.

                                       11
<PAGE>
THE TRADING PRICE OF OUR COMMON STOCK HAS BEEN VOLATILE AND MAY FLUCTUATE DUE TO
FACTORS BEYOND OUR CONTROL.

    The trading price of our common stock is subject to significant fluctuations
in response to numerous factors, including:

    - variations in anticipated or actual results of operations;

    - announcements of new products or technological innovations by competitors;

    - FDA approval or rejection of pending applications and regulatory
      enforcement actions;

    - changes in earnings estimates of operational results by analysts; and

    - results of clinical trials.

    Moreover, the stock market from time to time has experienced extreme price
and volume fluctuations, which have particularly affected the market prices for
emerging growth companies and which have often been unrelated to the operating
performance of these companies. These broad market fluctuations may adversely
affect the market price of our common stock. During the past two years from the
date of this prospectus, the market price per share of our common stock has
fluctuated between approximately $6.50 and $77.

                      WHERE YOU CAN FIND MORE INFORMATION

    We file annual, quarterly and special reports, proxy statements and other
information with the SEC. Our filings are available to the public over the
internet at the SEC's web site at http://www.sec.gov. You may also read and copy
any document we file at the SEC's Public Reference Rooms in Washington, D.C.,
New York, New York and Chicago, Illinois. The Public Reference Room in
Washington D.C. is located at 450 Fifth Street, N.W. Please call the SEC at
1-800-SEC-0330 for further information on the Public Reference Rooms.

    The SEC allows us to "incorporate by reference" the information we file with
it, which means that we can disclose important information to you by referring
you to those documents. The information incorporated by reference is an
important part of this prospectus, and information that we file later with the
SEC will automatically update and supersede this information. We incorporate by
reference the documents listed below and any future filings made with the SEC
under Sections 13(a), 13(c), 14, or 15(d) of the Securities Exchange Act of 1934
until the selling stockholders listed on page 16 sell all of our common stock
registered under this prospectus:

    - Annual Report on Form 10-K for the fiscal year ended December 31, 1999.

    - Quarterly Report on Form 10-Q/A for the quarter ended March 31, 2000.

    - Quarterly Report on Form 10-Q for the quarter ended June 30, 2000.

    - Quarterly Report on Form 10-Q for the quarter ended September 30, 2000.

    - Proxy Statement for the 2000 Annual Meeting of Stockholders.

    - Current Report on Form 8-K filed on December 23, 1999 as amended on
      January 7, 2000 and March 16, 2000.

    - Current Report on Form 8-K filed on August 17, 2000.

    - Current Report on Form 8-K filed on October 2, 2000.

    - The description of our common stock contained in our registration
      statement on Form 8-A, filed on January 18, 1996, including any amendment
      or report filed for the purpose of updating the description.

                                       12
<PAGE>
    - All other reports filed in accordance with Section 13(a) or 15(d) of the
      Securities Exchange Act of 1934 since December 31, 1999.

    This Prospectus is part of a registration statement on Form S-3 filed with
the SEC under the Securities Act of 1933. This prospectus does not contain all
of the information set forth in the registration statement. You should read the
registration statement for further information about SuperGen and our common
stock. You may request a copy of these filings at no cost. Please direct your
requests to:

    SuperGen, Inc.
    4140 Dublin Blvd., Suite 200
    Dublin, California 94568
    Attn: Investor Relations
    (925) 560-0100

    You should rely only on the information incorporated by reference or
provided in this Prospectus or any Prospectus Supplement. We have not authorized
anyone else to provide you with different information. You should not assume
that the information in this Prospectus or any Prospectus Supplement is accurate
as of any date other than the date on the front page of those documents.

                   NOTE REGARDING FORWARD-LOOKING STATEMENTS

    This Prospectus contains certain forward-looking statements within the
meaning of Section 27A of the Securities Act of 1933 and Section 21E of the
Securities Exchange Act of 1934. Forward-looking statements deal with our
current plans, intentions, beliefs and expectations and statements of future
economic performance. Statements containing terms such as "believes," "does not
believe," "plans," "expects," "intends," "estimates," "anticipates" and other
phrases of similar meaning are considered to contain uncertainty and are
forward-looking statements.

    Forward looking statements involve known and unknown risks and uncertainties
which may cause our actual results in future periods to differ materially from
what is currently anticipated. We make cautionary statements in certain sections
of this Prospectus, including under "Risk Factors." You should read these
cautionary statements as being applicable to all related forward-looking
statements wherever they appear in:

    - this Prospectus, in the materials referred to in this Prospectus;

    - in the materials incorporated by reference into this Prospectus;

    - in our press releases.

    No forward-looking statement is a guarantee of future performance and you
should not place undue reliance on any forward-looking statement.

                                USE OF PROCEEDS

    We will not receive any proceeds from the sale of the common stock by the
selling stockholders.

                                DIVIDEND POLICY

    We have not declared or paid cash dividends on our common stock. We
currently intend to retain all future earnings to fund the operation of our
business and, therefore, we do not anticipate paying dividends in the
foreseeable future. Future cash dividends, if any, will be determined by our
board of directors.

                                       13
<PAGE>
                              SELLING STOCKHOLDERS

    The following table shows information known to us about the beneficial
ownership of our common stock as of November 30, 2000, and as adjusted to
reflect the sale of common stock offered hereby by each selling stockholder
known by us to own beneficially the common stock. The table sets forth
information for each selling stockholder as follows:

    - The name of the selling stockholder;

    - The number of shares and the percentage the selling stockholder
      beneficially owns before this offering;

    - How many shares of common stock the selling stockholder may resell under
      this Prospectus; and

    - Assuming the selling stockholder sells all the shares listed next to its
      name, how many shares of common stock and the percentage the selling
      stockholder will beneficially own after completion of the offering.

    Beneficial ownership is determined in accordance with rules promulgated by
the SEC, and the information is not necessarily indicative of beneficial
ownership for any other purpose. Except as otherwise indicated, we believe that
the persons or entities named in the following table have sole voting and
investment power with respect to all shares of the common stock shown as
beneficially owned by them, subject to community property laws where applicable.
To prevent dilution to the selling stockholders, the following numbers may
change because of stock splits, stock dividends or similar events involving our
common stock.

    Within the past three years the following selling stockholders have held
positions or offices with us or have had material relationships with us other
than as a result of the ownership of our common stock:

    - In July 2000 we entered into a licensing and development agreement with
      AVI. Dr. Denis Burger is the Chairman and Chief Executive Officer of AVI
      and a member of our Board of Directors. Dr. Burger disclaims beneficial
      ownership of the shares of common stock held by AVI;

    - In October 2000 we purchased certain intellectual property assets from
      AMUR Pharmaceuticals, Inc., one of the selling stockholders, in exchange
      for stock and warrants.

    - Sandi Yurichuk, President of AMUR Pharmaceuticals, Inc., has been a
      consultant to us since April 15, 1999;

    - David Fineman, a beneficial owner of common stock through the Gunn Fineman
      Inc, Profit Sharing and Money Purchase Pension Trust and Fineman Revocable
      Trust, was one of our directors until May, 1998; and

    - J. Gregory Swendsen, the beneficial owner of common stock through the J.
      Gregory Swensen and Susan H. Bell Revocable Inter Vivos Trust, was one of
      our directors until July, 1998.

    As part of the consideration for our acquisition of AMUR intellectual
property, we issued warrants for the purchase of 200,000 shares of our common
stock with an exercise of $40 per share. These warrants expire on September 26,
2002. Under the terms of the AMUR transaction this prospectus

                                       14
<PAGE>
covers the sale by the selling stockholders of the 200,000 shares underlying
these warrants. We can not determine whether these warrants will be exercised or
if the underlying shares will be sold.

<TABLE>
<CAPTION>
                                                      SHARES OF COMMON                     SHARES OF COMMON
                                                     STOCK BENEFICIALLY                STOCK TO BE BENEFICIALLY
                                                     OWNED BEFORE OFFER                  OWNED AFTER OFFERING
                                                   UNDER THIS PROSPECTUS     SHARES      UNDER THIS PROSPECTUS
                                                   ----------------------    TO BE     -------------------------
NAME                                                NUMBER     PERCENTAGE   OFFERED      NUMBER      PERCENTAGE
----                                               ---------   ----------   --------   -----------   -----------
<S>                                                <C>         <C>          <C>        <C>           <C>
AVI BioPharma, Inc...............................    447,826      1.3%      347,826       100,000          *
Clayton Foundation for Research..................     46,613        *        46,613             0          0%
Stout & Company as Nominee for Research
  Development Foundation.........................     28,799        *        28,799             0          0%
Jesup & Lamont(1)................................     11,500        *        11,500             0          0%
Paulson Investment Company, Inc.(2)..............      5,000        *         5,000             0          0%
Scott Hamersly(3)................................     26,955        *         3,030        23,925          *
AMUR Pharmaceuticals, Inc........................        789        *           789             0          0%
Stockholders of AMUR Pharmaceuticals, Inc.:
  Gunn Fineman Inc, Profit Sharing and Money
    Purchase Pension Trust.......................     21,152        *         4,402        16,750          *
  Fineman Revocable Trust........................    402,549      1.2%        2,549       400,000        1.2%
  J. Gregory Swendsen and Susan H. Bell Revocable
    Inter Vivos Trust............................  1,097,145      3.3%        6,795     1,090,350        3.3%
  Wayne Hamersly(4)..............................    196,250        *        17,600       178,650          *
  Christian P. Erdman(5).........................    430,929      1.3%        7,626       423,000        1.3%
  Sandi Yurichuk(6)..............................     29,763        *        24,763         5,000          *
  All other stockholders of AMUR Pharmaceuticals,
    Inc. or their permitted assignees(7).........    190,241        *       190,241             0          0%
</TABLE>

--------------------------

*   REPRESENTS LESS THAN 1% OF THE OUTSTANDING COMMON STOCK OF THE COMPANY

(1) Represents 11,500 shares of common stock issuable upon exercise of a warrant
    to purchase common stock, all of which are being offered for sale pursuant
    to this Prospectus.

(2) Represents 5,000 shares of common stock issuable upon exercise of a warrant
    to purchase common stock, all of which are being offered for sale pursuant
    to this Prospectus.

(3) Includes 3,030 shares of common stock issuable upon exercise of a warrant
    held by Mr. Hamersly, all of which are being offered for sale pursuant to
    this Prospectus.

(4) Includes 630 shares of common stock issuable upon exercise of a warrant held
    by Mr. Hamersly and 16,970 shares of common stock issued to Mr. Hamersly
    upon exercise of a warrant privately issued to Mr. Hamersly, all of which
    are being offered for sale pursuant to this Prospectus.

(5) Includes 2,992 shares of common stock issuable upon exercise of a warrant
    held by Mr. Erdman, all of which are being offered for sale pursuant to this
    Prospectus.

(6) Includes 20,500 shares of common stock issuable upon exercise of a warrant
    held by Ms. Yurichuk, all of which are being offered for sale pursuant to
    this Prospectus. Also includes 5,000 shares of common stock issuable upon
    exercise of an option held by Ms. Yurichuk.

(7) Includes 176,508 shares of common stock issuable upon exercise of warrants
    held by stockholders of AMUR or their permitted assigns, all of which are
    being offered for sale pursuant to this Prospectus.

                              PLAN OF DISTRIBUTION

    We will not receive any proceeds from the sale of the shares. The shares are
being offered on behalf of the selling stockholders. The shares may be sold or
distributed from time to time by the selling stockholders, or by pledgees,
donees or transferees of, or other successors in interest to, the selling
stockholders, directly to one or more purchasers (including pledgees) or through
brokers, dealers or underwriters who may act solely as agents or may acquire
shares as principals, at market prices prevailing at the time of sale, at prices
related to such prevailing market prices, at negotiated prices, or at fixed
prices, which may be changed.

                                       15
<PAGE>
    The sale of the shares may be effected in one or more of the following
methods:

    - ordinary brokers' transactions, which may include long or short sales;

    - transactions involving cross or block trades or otherwise on the Nasdaq
      National Stock Market;

    - purchases by brokers, dealers or underwriters as principal and resale by
      such purchasers for their own accounts pursuant to this prospectus;

    - "at the market" to or through market makers or into an existing market for
      the shares;

    - in other ways not involving market makers or established trading markets,
      including direct sales to purchases or sales effected through agents;

    - through transactions in options, swaps or other derivatives (whether
      exchange-listed or otherwise); or

    - any combination of the foregoing, or by any other legally available means.

    In addition, the selling stockholders or their successors in interest may
enter into hedging transactions with broker-dealers who may engage in short
sales of shares in the course of hedging the positions they assume with the
selling stockholders. The selling stockholders or their successors in interest
may also enter into option or other transactions with broker-dealers that
require the delivery by such broker-dealers of the shares, which shares may be
resold thereafter pursuant to this prospectus.

    Brokers, dealers, underwriters or agents participating in the distribution
of the shares as agents may receive compensation in the form of commissions,
discounts or concessions from the selling stockholders and/or purchasers of the
shares for whom such broker-dealers may act as agent, or to whom they may sell
as principal, or both (which compensation as to a particular broker-dealer may
be less than or in excess of customary commissions). The selling stockholders
and any broker-dealers who act in connection with the sale of shares hereunder
may be deemed to be "Underwriters" within the meaning of the Securities Act, and
any commissions they receive and proceeds of any sale of shares may be deemed to
be underwriting discounts and commissions under the securities act. Neither
SuperGen nor any selling stockholder can presently estimate the amount of such
compensation. SuperGen knows of no existing arrangements between any selling
stockholder, any other stockholder, broker, dealer, underwriter or agent
relating to the sale or distribution of the shares.

                                 LEGAL MATTERS

    The validity of the issuance of common stock will be passed upon for us by
Wilson Sonsini Goodrich & Rosati, P.C., Palo Alto, California.

                                    EXPERTS

    Ernst & Young LLP, independent auditors, have audited our consolidated
financial statements included in our Annual Report on Form 10-K for the year
ended December 31, 1999, as set forth in their report, which is incorporated by
reference in this prospectus and elsewhere in the registration statement. Our
financial statements are incorporated by reference in reliance on Ernst & Young
LLP's report, given on their authority as experts in accounting and auditing.

                                       16
<PAGE>
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------

    NO DEALER, SALESPERSON OR OTHER PERSON IS AUTHORIZED TO GIVE ANY INFORMATION
OR TO REPRESENT ANYTHING NOT CONTAINED IN THIS PROSPECTUS. YOU MUST NOT RELY ON
ANY UNAUTHORIZED INFORMATION OR REPRESENTATIONS. THIS PROSPECTUS IS AN OFFER TO
SELL ONLY THE SHARES OFFERED HEREBY, BUT ONLY UNDER CIRCUMSTANCES AND IN
JURISDICTIONS WHERE IT IS LAWFUL TO DO SO. THE INFORMATION CONTAINED IN THIS
PROSPECTUS IS CURRENT ONLY AS OF ITS DATE.

                            ------------------------

                               TABLE OF CONTENTS

<TABLE>
<CAPTION>
                                          PAGE
                                        --------
<S>                                     <C>
Summary...............................      2

Risk Factors..........................      4

Where You Can Find More Information...     12

Note Regarding Forward-Looking
  Statements..........................     13

Use of Proceeds.......................     13

Dividend Policy.......................     13

Selling Stockholders..................     14

Plan Of Distribution..................     15

Legal Matters.........................     16

Experts...............................     16
</TABLE>

                                 697,533 SHARES

                                 SUPERGEN, INC.

                                  COMMON STOCK

                             ---------------------

                                   PROSPECTUS

                             ---------------------

                               DECEMBER 20, 2000

--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
<PAGE>
                                    PART II

                     INFORMATION NOT REQUIRED IN PROSPECTUS

ITEM 14. OTHER EXPENSES OF ISSUANCE AND DISTRIBUTION.

    The Registrant will pay all reasonable expenses incident to the registration
of the shares other than any commissions and discounts of underwriters, dealers
or agents. Such expenses are set forth in the following table. All of the
amounts shown are estimates except the SEC registration fee.

<TABLE>
<CAPTION>
                                                              AMOUNT TO BE PAID
                                                              -----------------
<S>                                                           <C>
SEC registration fee........................................       $ 3,597
Legal fees and expenses.....................................        10,000
Accounting fees and expense.................................         7,500
                                                                   -------
Total.......................................................       $21,097
                                                                   -------
</TABLE>

ITEM 15. INDEMNIFICATION OF DIRECTORS AND OFFICERS.

    Section 145 of the Delaware General Corporation's Law authorizes a
corporation to indemnify its directors, officers, employees or other agents in
terms sufficiently broad to permit indemnification (including reimbursement for
expenses incurred) under certain circumstances for liabilities arising under the
Securities Act. The Registrant's Certificate of Incorporation (Exhibit 3.1
hereto) and Bylaws (Exhibit 3.2 hereto) provide indemnification of its directors
and officers to the maximum extent permitted by the Delaware General Corporation
Law. In addition, the Registrant has entered into Indemnification Agreements
with its directors and officers.

    Under the Registration Rights Agreement (Exhibits 4.1 hereto), the
Registrant has agreed to indemnify the selling stockholders and persons
controlling the selling stockholders against certain liabilities, including
liabilities under the Securities Act of 1933, and the selling stockholders have
agreed to indemnify the Registrant, its directors, its officers and certain
control and related persons against certain liabilities, including liabilities
under the Securities Act of 1933.

ITEM 16. EXHIBITS.

<TABLE>
<CAPTION>
       EXHIBIT
       NUMBER                             DESCRIPTION OF DOCUMENT
---------------------   ------------------------------------------------------------
<C>                     <S>
       3.1(a)           Amended and Restated Certificate of Incorporation of the
                        Registrant

       3.2(b)           Bylaws, as amended, of the Registrant

       4.1              Registration Rights Agreement dated April 4, 2000 between
                        the Registrant and AVI BioPharma, Inc.

       4.2*(c)          Research Agreement (Camptothecin) dated November 15, 1999
                        between the Registrant and Clayton Foundation for Research.

       4.3*(c)          Research Agreement (Paclitaxel) dated November 15, 1999
                        between the Registrant and Clayton Foundation for Research.

       4.4*(c)          License Agreement (Camptothecin) dated November 15, 1999
                        between the Registrant and Research Development Foundation.

       4.5*(c)          License Agreement (Paclitaxel) dated November 15, 1999
                        between the Registrant and Research Development Foundation.

       4.6              Registration Rights Agreement dated September 27, 2000
                        between the Registrant and AMUR Pharmaceuticals, Inc.

       4.7              Warrant Agreement dated December 23, 1998 between the
                        Registrant and Jessup & Lamont Securities Corporation
</TABLE>

                                      II-1
<PAGE>

<TABLE>
<CAPTION>
       EXHIBIT
       NUMBER                             DESCRIPTION OF DOCUMENT
---------------------   ------------------------------------------------------------
<C>                     <S>
       4.8              Warrant Agreement dated October 4, 1999 between the
                        Registrant and Paulson Investment Company, Inc.

       5.1              Opinion of Wilson Sonsini Goodrich & Rosati, P.C.

      23.1              Consent of Ernst & Young LLP, Independent Auditors

      23.4              Consent of Counsel (included in Exhibit 5.1)

      24.1              Power of Attorney (included on page II-4)
</TABLE>

------------------------

(a) Incorporated by reference from the Registrant's Report on Form 10-Q filed
    with the Securities and Exchange Commission on August 11, 2000.

(b) Incorporated by reference from the Registrant's Report on Form 10-K filed
    with the Securities and Exchange Commission on March 19, 1998.

(c) Incorporated by reference from the Registrant's Registration Statement on
    Form S-3 (reg. No. 333-95177) filed with the Securities and Exchange
    Commission January 21, 2000 and amended on March 16, 2000.

*   Confidential treatment has been previously granted for certain portions of
    these exhibits.

ITEM 17. UNDERTAKINGS.

    SuperGen hereby undertakes:

    1.  To file, during any period in which offers or sales are being made, a
post-effective amendment to this Registration Statementto include any material
information with respect to the plan of distribution not previously disclosed in
the registration statement or any material change to such information in the
registration statement.

    2.  That, for the purpose of determining any liability under the Securities
Act, each such post-effective amendment shall be deemed to be a new registration
statement relating to the securities offered therein, and the offering of such
securities at that time shall be deemed to be the initial bona fide offering
thereof.

    3.  To remove from registration by means of a post-effective amendment any
of the securities being registered which remain unsold at the termination of the
offering.

    4.  That, for purposes of determining any liability under the Securities
Act, each filing of our annual report pursuant to Section 13(a) or
Section 15(d) of the Exchange Act, (and, where applicable, each filing of an
employee benefit plan's annual report pursuant to Section 15(d) of the Exchange
Act) that is incorporated by reference in the registration statement shall be
deemed to be a new registration statement relating to the securities offered
therein, and the offering of such securities at that time shall be deemed to be
the initial bona fide offering thereof.

    5.  Insofar as indemnification for liabilities arising under the Securities
Act may be permitted to directors, officers and controlling persons of SuperGen
pursuant to the foregoing provisions, or otherwise, SuperGen has been advised
that in the opinion of the SEC such indemnification is against public policy as
expressed in the Securities Act and is, therefore, unenforceable. In the event
that a claim for indemnification against such liabilities (other than the
payment by SuperGen of expenses incurred or paid by a director, officer, or
controlling person of SuperGen in the successful defense of any action, suit, or
proceeding) is asserted by such director, officer, or controlling person in
connection with the securities being registered, SuperGen will, unless in the
opinion of its counsel the matter has been settled by controlling precedent,
submit to a court of appropriate jurisdiction the question whether such
indemnification by it is against public policy as expressed in the Securities
Act and will be governed by the final adjudication of such issue.

                                      II-2
<PAGE>
                                   SIGNATURES

    Pursuant to the requirements of the Securities Act of 1933, the Registrant
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-3 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the city of Dublin, state of California, on December 20, 2000.

<TABLE>
<S>                                                    <C>  <C>
                                                       SUPERGEN, INC.

                                                       By:            /s/ JOSEPH RUBINFELD
                                                            ----------------------------------------
                                                                     Joseph Rubinfeld, Ph.D.
                                                                    CHIEF EXECUTIVE OFFICER,
                                                                     PRESIDENT AND DIRECTOR
</TABLE>

                               POWER OF ATTORNEY

    Each person whose signature appears below constitutes and appoints Joseph
Rubinfeld and Ronald H. Spair, and each of them individually, as
attorney-in-fact, with the power of substitution, for him in any and all
capacities, to sign any amendment to this Registration Statement and to file the
same, with exhibits thereto and other documents in connection therewith, with
the Securities and Exchange Commission, granting to said attorney-in-fact full
power and authority to do and perform each and every act and thing requisite and
necessary to be done in connection therewith, as fully to all intents and
purposes as he might or could do in person, hereby ratifying and confirming all
that said attorney-in-fact or any of them, or their, his or her substitute or
substitutes, may lawfully do or cause to be done by virtue hereof.

    Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed below by the following persons in the
capacities and on the dates indicated.

<TABLE>
<CAPTION>
              SIGNATURE                                  TITLE                          DATE
              ---------                                  -----                          ----
<C>                                    <S>                                        <C>
        /s/ JOSEPH RUBINFELD           Chief Executive Officer, President and     December 20, 2000
    ----------------------------       Director (Principal Executive Officer)
          Joseph Rubinfeld

         /s/ RONALD H. SPAIR           Chief Financial Officer (Principal         December 20, 2000
    ----------------------------       Financial and Accounting Officer)
           Ronald H. Spair

          /s/ DENIS BURGER
    ----------------------------       Director                                   December 20, 2000
            Denis Burger

        /s/ THOMAS V. GIRARDI
    ----------------------------       Director                                   December 20, 2000
          Thomas V. Girardi

         /s/ WALTER J. LACK
    ----------------------------       Director                                   December 20, 2000
           Walter J. Lack

           /s/ DANIEL ZURR
    ----------------------------       Director                                   December 20, 2000
             Daniel Zurr
</TABLE>

                                      II-3
<PAGE>
                                 EXHIBIT INDEX

<TABLE>
<CAPTION>
       EXHIBIT
       NUMBER                             DESCRIPTION OF DOCUMENT
---------------------   ------------------------------------------------------------
<C>                     <S>
       3.1(a)           Amended and Restated Certificate of Incorporation of the
                        Registrant

       3.2(b)           Bylaws, as amended, of the Registrant

       4.1              Registration Rights Agreement dated April 4, 2000 between
                        the Registrant and AVI BioPharma, Inc.

       4.2*(c)          Research Agreement (Camptothecin) dated November 15, 1999
                        between the Registrant and Clayton Foundation for Research.

       4.3*(c)          Research Agreement (Paclitaxel) dated November 15, 1999
                        between the Registrant and Clayton Foundation for Research.

       4.4*(c)          License Agreement (Camptothecin) dated November 15, 1999
                        between the Registrant and Research Development Foundation.

       4.5*(c)          License Agreement (Paclitaxel) dated November 15, 1999
                        between the Registrant and Research Development Foundation.

       4.6              Registration Rights Agreement dated September 27, 2000
                        between the Registrant and AMUR Pharmaceuticals, Inc.

       4.7              Warrant Agreement dated December 23, 1998 between the
                        Registrant and Jessup & Lamont Securities Corporation

       4.8              Warrant Agreement dated October 4, 1999 between the
                        Registrant and Paulson Investment Company, Inc.

       5.1              Opinion of Wilson Sonsini Goodrich & Rosati, P.C.

      23.1              Consent of Ernst & Young LLP, Independent Auditors

      23.4              Consent of Counsel (included in Exhibit 5.1)

      24.1              Power of Attorney (included on page II-4)
</TABLE>

------------------------

(a) Incorporated by reference from the Registrant's Report on Form 10-Q filed
    with the Securities and Exchange Commission on August 11, 2000.

(b) Incorporated by reference from the Registrant's Report on Form 10-K filed
    with the Securities and Exchange Commission on March 19, 1998.

(c) Incorporated by reference from the Registrant's Registration Statement on
    Form S-3 (reg. No. 333-95177) filed with the Securities and Exchange
    Commission January 21, 2000 and amended on March 16, 2000.

*   Confidential treatment has been previously granted for certain portions of
    these exhibits.


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